Starting phenix.real_space_refine on Sun Jul 5 21:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtp_65338/07_2026/9vtp_65338.cif" } resolution = 2.68 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= 0.000 sd= 0.047 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 P 97 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 18619 2.51 5 N 5150 2.21 5 O 5809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29818 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1221 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 7, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 24, 'rna3p': 32} Chain breaks: 1 Chain: "2" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 721 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "3" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2725 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2767 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2771 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain: "E" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2767 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain: "F" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2418 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2374 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 306} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2051 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2911 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 365} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 6, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 149 Chain: "J" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2670 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 340} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 8, 'PHE:plan': 5, 'ASN:plan1': 7, 'GLU:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 2, 'TRP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 29818 At special positions: 0 Unit cell: (130.096, 193.264, 164.688, 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) S 142 16.00 P 97 15.00 Mg 1 11.99 O 5809 8.00 N 5150 7.00 C 18619 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 47 sheets defined 37.5% alpha, 16.3% beta 31 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 139 through 147 removed outlier: 6.414A pdb=" N ARG A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 146 " --> pdb=" O TRP A 143 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 147 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 300 through 307 removed outlier: 3.811A pdb=" N LYS A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 6.406A pdb=" N ARG B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.516A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 322 through 339 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.772A pdb=" N ALA C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 300 through 307 removed outlier: 3.615A pdb=" N LEU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 removed outlier: 3.544A pdb=" N ALA C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'D' and resid 45 through 50 removed outlier: 4.369A pdb=" N ALA D 49 " --> pdb=" O GLY D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 185 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.632A pdb=" N TYR E 50 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.520A pdb=" N GLN E 67 " --> pdb=" O SER E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.542A pdb=" N LEU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 300 through 306 Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 322 through 339 Processing helix chain 'F' and resid 105 through 123 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.530A pdb=" N ARG F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 300 through 307 removed outlier: 3.700A pdb=" N LYS F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.712A pdb=" N GLN F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 Processing helix chain 'G' and resid 4 through 10 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 35 through 47 removed outlier: 3.529A pdb=" N ALA G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 53 removed outlier: 6.401A pdb=" N ILE G 51 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.811A pdb=" N ASP G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 81 removed outlier: 3.670A pdb=" N THR G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS G 80 " --> pdb=" O PHE G 76 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 127 through 135 removed outlier: 3.544A pdb=" N MET G 130 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN G 131 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER G 133 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE G 135 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.812A pdb=" N ASN G 162 " --> pdb=" O HIS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 184 Processing helix chain 'G' and resid 219 through 230 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 249 through 254 removed outlier: 4.074A pdb=" N CYS G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 293 Processing helix chain 'G' and resid 301 through 324 removed outlier: 3.561A pdb=" N GLN G 322 " --> pdb=" O MET G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 383 through 389 Processing helix chain 'G' and resid 415 through 434 removed outlier: 4.079A pdb=" N ALA G 433 " --> pdb=" O ASN G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 503 Processing helix chain 'G' and resid 516 through 520 Processing helix chain 'G' and resid 528 through 535 Processing helix chain 'G' and resid 554 through 565 Processing helix chain 'G' and resid 587 through 591 Processing helix chain 'G' and resid 613 through 617 Processing helix chain 'H' and resid 16 through 36 removed outlier: 3.575A pdb=" N ILE H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.748A pdb=" N LEU H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 104 through 109 removed outlier: 4.205A pdb=" N ASP H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'I' and resid 17 through 30 removed outlier: 3.569A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 43 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.974A pdb=" N LYS I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 87 removed outlier: 3.639A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS I 81 " --> pdb=" O HIS I 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN I 84 " --> pdb=" O HIS I 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE I 87 " --> pdb=" O SER I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'I' and resid 132 through 139 removed outlier: 4.142A pdb=" N LEU I 136 " --> pdb=" O CYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.606A pdb=" N TRP I 146 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE I 148 " --> pdb=" O ARG I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 207 Processing helix chain 'I' and resid 219 through 233 removed outlier: 3.687A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET I 227 " --> pdb=" O ARG I 223 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS I 228 " --> pdb=" O TRP I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 270 Processing helix chain 'I' and resid 279 through 284 removed outlier: 3.886A pdb=" N ILE I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 292 removed outlier: 3.806A pdb=" N SER I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE I 292 " --> pdb=" O LEU I 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 287 through 292' Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 331 through 336 Processing helix chain 'I' and resid 340 through 350 removed outlier: 3.548A pdb=" N VAL I 344 " --> pdb=" O SER I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 384 Processing helix chain 'I' and resid 391 through 395 removed outlier: 3.822A pdb=" N PHE I 394 " --> pdb=" O ASN I 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 29 Processing helix chain 'J' and resid 33 through 49 removed outlier: 3.969A pdb=" N PHE J 37 " --> pdb=" O ASP J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 71 through 85 Processing helix chain 'J' and resid 132 through 138 Processing helix chain 'J' and resid 143 through 147 Processing helix chain 'J' and resid 197 through 207 Processing helix chain 'J' and resid 219 through 234 removed outlier: 4.626A pdb=" N MET J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS J 228 " --> pdb=" O TRP J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 263 Processing helix chain 'J' and resid 266 through 271 removed outlier: 3.646A pdb=" N CYS J 271 " --> pdb=" O ASN J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 289 removed outlier: 8.043A pdb=" N LYS J 286 " --> pdb=" O ASP J 282 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE J 287 " --> pdb=" O ILE J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 315 removed outlier: 3.899A pdb=" N LYS J 306 " --> pdb=" O ASN J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 337 removed outlier: 3.641A pdb=" N LEU J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 351 Processing helix chain 'J' and resid 374 through 384 Processing helix chain 'J' and resid 391 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 23 current: chain 'A' and resid 151 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 94 current: chain 'A' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 24 current: chain 'B' and resid 151 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.795A pdb=" N ARG B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 94 current: chain 'B' and resid 243 through 246 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AB1, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.716A pdb=" N TYR B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 243 through 246 Processing sheet with id=AB6, first strand: chain 'C' and resid 34 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AB8, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.633A pdb=" N TYR C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.557A pdb=" N LYS D 102 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.593A pdb=" N SER D 84 " --> pdb=" O ASN D 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 23 current: chain 'D' and resid 151 through 158 Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.593A pdb=" N SER D 84 " --> pdb=" O ASN D 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 94 current: chain 'D' and resid 243 through 246 Processing sheet with id=AC3, first strand: chain 'D' and resid 34 through 42 Processing sheet with id=AC4, first strand: chain 'D' and resid 265 through 267 Processing sheet with id=AC5, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC6, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 151 through 158 Processing sheet with id=AC8, first strand: chain 'E' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 243 through 246 Processing sheet with id=AC9, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 284 through 285 removed outlier: 4.083A pdb=" N TYR E 290 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AD3, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AD4, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AD5, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AD6, first strand: chain 'F' and resid 243 through 246 Processing sheet with id=AD7, first strand: chain 'F' and resid 283 through 284 Processing sheet with id=AD8, first strand: chain 'G' and resid 30 through 31 removed outlier: 6.298A pdb=" N VAL G 30 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 85 through 86 removed outlier: 4.590A pdb=" N VAL G 217 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AE2, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.118A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL G 444 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LEU G 546 " --> pdb=" O PHE G 442 " (cutoff:3.500A) removed outlier: 14.263A pdb=" N PHE G 442 " --> pdb=" O LEU G 546 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU G 440 " --> pdb=" O SER G 490 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N SER G 490 " --> pdb=" O GLU G 440 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE G 442 " --> pdb=" O ARG G 488 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG G 488 " --> pdb=" O PHE G 442 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL G 444 " --> pdb=" O ILE G 486 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE G 486 " --> pdb=" O VAL G 444 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE G 446 " --> pdb=" O SER G 484 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER G 484 " --> pdb=" O ILE G 446 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS G 479 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY G 401 " --> pdb=" O CYS G 479 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU G 485 " --> pdb=" O PRO G 395 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU G 487 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU G 393 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS G 489 " --> pdb=" O TYR G 391 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR G 391 " --> pdb=" O CYS G 489 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.118A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 599 " --> pdb=" O GLY G 574 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY G 574 " --> pdb=" O ILE G 599 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY G 601 " --> pdb=" O CYS G 572 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N CYS G 572 " --> pdb=" O GLY G 601 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE G 603 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL G 570 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE G 605 " --> pdb=" O GLN G 568 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN G 568 " --> pdb=" O PHE G 605 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 236 through 240 removed outlier: 8.286A pdb=" N ILE G 411 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE G 261 " --> pdb=" O ILE G 411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 461 through 462 Processing sheet with id=AE6, first strand: chain 'G' and resid 619 through 624 Processing sheet with id=AE7, first strand: chain 'H' and resid 41 through 43 Processing sheet with id=AE8, first strand: chain 'H' and resid 100 through 103 removed outlier: 5.343A pdb=" N ASN H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER H 156 " --> pdb=" O ASN H 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 98 through 104 removed outlier: 4.501A pdb=" N ALA I 111 " --> pdb=" O ASN I 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 327 through 328 Processing sheet with id=AF2, first strand: chain 'J' and resid 98 through 100 1071 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8091 1.33 - 1.45: 6575 1.45 - 1.58: 15706 1.58 - 1.70: 192 1.70 - 1.82: 188 Bond restraints: 30752 Sorted by residual: bond pdb=" C3' DG 2 27 " pdb=" C2' DG 2 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT 2 32 " pdb=" C2' DT 2 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DC 2 28 " pdb=" C2' DC 2 28 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG 2 37 " pdb=" C2' DG 2 37 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DA 2 26 " pdb=" C2' DA 2 26 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.42e+00 ... (remaining 30747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 41593 2.08 - 4.16: 529 4.16 - 6.24: 61 6.24 - 8.33: 11 8.33 - 10.41: 7 Bond angle restraints: 42201 Sorted by residual: angle pdb=" C ASN I 241 " pdb=" CA ASN I 241 " pdb=" CB ASN I 241 " ideal model delta sigma weight residual 115.79 110.18 5.61 1.19e+00 7.06e-01 2.22e+01 angle pdb=" N3 DT 2 55 " pdb=" C4 DT 2 55 " pdb=" O4 DT 2 55 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT 2 24 " pdb=" C4 DT 2 24 " pdb=" O4 DT 2 24 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" O4 DT 2 55 " pdb=" C4 DT 2 55 " pdb=" C5 DT 2 55 " ideal model delta sigma weight residual 124.90 122.01 2.89 7.00e-01 2.04e+00 1.71e+01 angle pdb=" N3 DT 2 36 " pdb=" C4 DT 2 36 " pdb=" O4 DT 2 36 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 42196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.41: 15302 18.41 - 36.82: 2030 36.82 - 55.23: 663 55.23 - 73.65: 172 73.65 - 92.06: 50 Dihedral angle restraints: 18217 sinusoidal: 7825 harmonic: 10392 Sorted by residual: dihedral pdb=" O4' C 1 34 " pdb=" C1' C 1 34 " pdb=" N1 C 1 34 " pdb=" C2 C 1 34 " ideal model delta sinusoidal sigma weight residual -160.00 -82.54 -77.46 1 1.50e+01 4.44e-03 3.34e+01 dihedral pdb=" O4' C 1 24 " pdb=" C1' C 1 24 " pdb=" N1 C 1 24 " pdb=" C2 C 1 24 " ideal model delta sinusoidal sigma weight residual -160.00 -102.63 -57.37 1 1.50e+01 4.44e-03 1.97e+01 dihedral pdb=" O4' C 1 15 " pdb=" C1' C 1 15 " pdb=" N1 C 1 15 " pdb=" C2 C 1 15 " ideal model delta sinusoidal sigma weight residual -128.00 -63.16 -64.84 1 1.70e+01 3.46e-03 1.91e+01 ... (remaining 18214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4033 0.059 - 0.119: 554 0.119 - 0.178: 51 0.178 - 0.237: 0 0.237 - 0.296: 1 Chirality restraints: 4639 Sorted by residual: chirality pdb=" CG LEU J 46 " pdb=" CB LEU J 46 " pdb=" CD1 LEU J 46 " pdb=" CD2 LEU J 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1' C 1 34 " pdb=" O4' C 1 34 " pdb=" C2' C 1 34 " pdb=" N1 C 1 34 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" C3' DA 2 29 " pdb=" C4' DA 2 29 " pdb=" O3' DA 2 29 " pdb=" C2' DA 2 29 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4636 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 6 " -0.033 2.00e-02 2.50e+03 1.56e-02 6.65e+00 pdb=" N9 A 1 6 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 1 6 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 6 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 6 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 1 6 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 6 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 11 " 0.033 2.00e-02 2.50e+03 1.45e-02 6.26e+00 pdb=" N9 G 1 11 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G 1 11 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 1 11 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 11 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 11 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 1 11 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G 1 11 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 1 11 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 1 11 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 1 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G 1 11 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 23 " 0.026 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" N1 U 1 23 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U 1 23 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U 1 23 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U 1 23 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U 1 23 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U 1 23 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U 1 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U 1 23 " -0.004 2.00e-02 2.50e+03 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5057 2.77 - 3.30: 28545 3.30 - 3.83: 51482 3.83 - 4.37: 61232 4.37 - 4.90: 102068 Nonbonded interactions: 248384 Sorted by model distance: nonbonded pdb=" OP2 A 1 6 " pdb="MG MG 1 101 " model vdw 2.236 2.170 nonbonded pdb=" N GLU G 268 " pdb=" OE1 GLU G 268 " model vdw 2.445 3.120 nonbonded pdb=" O5' DG 2 53 " pdb=" O4' DG 2 53 " model vdw 2.493 2.432 nonbonded pdb=" O GLU G 561 " pdb=" OE1 GLU G 561 " model vdw 2.502 3.040 nonbonded pdb=" O2' C 1 34 " pdb=" O4' U 1 35 " model vdw 2.505 3.040 ... (remaining 248379 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 'A' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'B' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'C' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'D' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'E' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 13 through 84 or (resid 85 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 209 or (resid 210 throu \ gh 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thr \ ough 229 or (resid 230 through 242 and (name N or name CA or name C or name O or \ name CB )) or resid 243 through 251 or (resid 252 through 260 and (name N or na \ me CA or name C or name O or name CB )) or resid 261 or (resid 262 through 284 a \ nd (name N or name CA or name C or name O or name CB )) or resid 285 or (resid 2 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 287 through \ 319 or resid 330 through 356 or resid 373 through 395)) selection = (chain 'J' and ((resid 13 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 23 or (resid 24 and (name N or na \ me CA or name C or name O or name CB )) or resid 25 through 26 or (resid 27 and \ (name N or name CA or name C or name O or name CB )) or resid 28 through 31 or ( \ resid 32 through 63 and (name N or name CA or name C or name O or name CB )) or \ resid 64 through 189 or (resid 190 through 202 and (name N or name CA or name C \ or name O or name CB )) or resid 203 through 247 or (resid 248 and (name N or na \ me CA or name C or name O or name CB )) or resid 249 through 395)) } 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: 6.480 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.650 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30752 Z= 0.181 Angle : 0.583 10.406 42201 Z= 0.351 Chirality : 0.042 0.296 4639 Planarity : 0.004 0.057 5094 Dihedral : 19.245 92.057 11511 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.79 % Allowed : 32.31 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.18 (0.14), residues: 3498 helix: 1.11 (0.16), residues: 1135 sheet: 0.40 (0.22), residues: 585 loop : -1.13 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.018 0.001 TYR I 171 PHE 0.025 0.001 PHE J 309 TRP 0.020 0.001 TRP J 381 HIS 0.004 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.18 (30752) covalent geometry : angle 0.58317 / 0.35 (42201) hydrogen bonds : bond 0.13207 / 13.27 ( 1116) hydrogen bonds : angle 5.43401 / 6.73 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8546 (mt0) cc_final: 0.8146 (mt0) REVERT: A 324 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: A 342 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8854 (pt) REVERT: B 47 LYS cc_start: 0.9153 (tppt) cc_final: 0.8647 (tppt) REVERT: B 185 ASP cc_start: 0.8836 (m-30) cc_final: 0.8599 (p0) REVERT: C 313 GLU cc_start: 0.8807 (pp20) cc_final: 0.8398 (pp20) REVERT: D 105 ASP cc_start: 0.8668 (t0) cc_final: 0.8168 (t0) REVERT: D 202 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: E 53 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8459 (p0) REVERT: E 154 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9064 (mm) REVERT: F 215 PHE cc_start: 0.8666 (m-10) cc_final: 0.8413 (m-10) REVERT: H 188 THR cc_start: 0.5048 (OUTLIER) cc_final: 0.4658 (t) REVERT: I 121 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6123 (ttt-90) REVERT: I 122 SER cc_start: 0.7358 (m) cc_final: 0.6831 (t) REVERT: I 138 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5472 (mt-10) REVERT: I 172 ASP cc_start: 0.4786 (OUTLIER) cc_final: 0.3918 (m-30) REVERT: J 181 VAL cc_start: 0.6486 (t) cc_final: 0.6258 (m) REVERT: J 330 MET cc_start: 0.6697 (mpm) cc_final: 0.6157 (ptt) REVERT: J 353 LEU cc_start: 0.2309 (OUTLIER) cc_final: 0.1499 (mt) outliers start: 81 outliers final: 55 residues processed: 274 average time/residue: 0.5604 time to fit residues: 185.7666 Evaluate side-chains 249 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 121 ARG Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082559 restraints weight = 56615.171| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.37 r_work: 0.3068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30752 Z= 0.147 Angle : 0.530 8.479 42201 Z= 0.285 Chirality : 0.041 0.227 4639 Planarity : 0.004 0.058 5094 Dihedral : 14.909 88.892 5222 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.59 % Allowed : 29.24 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.10 (0.14), residues: 3498 helix: 1.20 (0.16), residues: 1158 sheet: 0.41 (0.22), residues: 592 loop : -1.13 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 110 TYR 0.015 0.001 TYR E 52 PHE 0.016 0.001 PHE E 302 TRP 0.013 0.001 TRP J 381 HIS 0.010 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (30752) covalent geometry : angle 0.52954 / 0.29 (42201) hydrogen bonds : bond 0.04360 / 4.08 ( 1116) hydrogen bonds : angle 4.66505 / 5.91 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 195 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8776 (mt0) cc_final: 0.8460 (mt0) REVERT: A 109 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8498 (tttm) REVERT: A 342 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8941 (pt) REVERT: B 47 LYS cc_start: 0.9281 (tppt) cc_final: 0.8886 (tppt) REVERT: B 55 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7833 (pp30) REVERT: B 231 ASP cc_start: 0.7659 (p0) cc_final: 0.7433 (p0) REVERT: C 313 GLU cc_start: 0.8845 (pp20) cc_final: 0.8467 (pp20) REVERT: D 1 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6982 (ttm) REVERT: D 105 ASP cc_start: 0.8638 (t0) cc_final: 0.8048 (t0) REVERT: D 202 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: D 325 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8175 (ttp) REVERT: E 53 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8478 (p0) REVERT: E 86 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8718 (tp30) REVERT: F 215 PHE cc_start: 0.8729 (m-10) cc_final: 0.8484 (m-10) REVERT: F 344 GLN cc_start: 0.8072 (tt0) cc_final: 0.7852 (tt0) REVERT: G 105 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8054 (m90) REVERT: G 260 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: H 29 HIS cc_start: 0.5494 (t70) cc_final: 0.5143 (t70) REVERT: H 31 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: H 188 THR cc_start: 0.5210 (OUTLIER) cc_final: 0.4999 (t) REVERT: I 163 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.4485 (tp30) REVERT: I 172 ASP cc_start: 0.3775 (p0) cc_final: 0.2899 (m-30) REVERT: I 317 TRP cc_start: 0.6710 (m-90) cc_final: 0.6359 (m-90) REVERT: J 28 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5683 (tttt) REVERT: J 69 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mmpt) REVERT: J 146 TRP cc_start: 0.8066 (m-10) cc_final: 0.7791 (m-10) REVERT: J 222 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.4869 (m-80) REVERT: J 330 MET cc_start: 0.6913 (mpm) cc_final: 0.6282 (ptt) outliers start: 162 outliers final: 68 residues processed: 336 average time/residue: 0.5254 time to fit residues: 215.8768 Evaluate side-chains 270 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 186 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 218 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 310 GLN J 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083622 restraints weight = 57387.992| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.41 r_work: 0.3094 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30752 Z= 0.106 Angle : 0.502 8.002 42201 Z= 0.271 Chirality : 0.040 0.261 4639 Planarity : 0.004 0.060 5094 Dihedral : 14.748 89.820 5169 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.34 % Allowed : 30.00 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.02 (0.14), residues: 3498 helix: 1.30 (0.16), residues: 1160 sheet: 0.44 (0.22), residues: 592 loop : -1.10 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.015 0.001 TYR H 138 PHE 0.013 0.001 PHE E 302 TRP 0.012 0.001 TRP J 381 HIS 0.012 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (30752) covalent geometry : angle 0.50242 / 0.27 (42201) hydrogen bonds : bond 0.03833 / 3.56 ( 1116) hydrogen bonds : angle 4.48838 / 5.65 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 203 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8731 (mt0) cc_final: 0.8400 (mt0) REVERT: A 342 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8912 (pt) REVERT: B 47 LYS cc_start: 0.9254 (tppt) cc_final: 0.8837 (tppt) REVERT: B 55 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7811 (pp30) REVERT: D 105 ASP cc_start: 0.8554 (t0) cc_final: 0.7981 (t0) REVERT: D 163 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.6660 (p0) REVERT: D 325 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: E 53 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8464 (p0) REVERT: E 86 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8672 (tp30) REVERT: E 287 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8354 (tm-30) REVERT: F 215 PHE cc_start: 0.8704 (m-10) cc_final: 0.8494 (m-10) REVERT: F 344 GLN cc_start: 0.8036 (tt0) cc_final: 0.7822 (tt0) REVERT: G 105 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.8015 (m90) REVERT: G 260 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: H 29 HIS cc_start: 0.5607 (t70) cc_final: 0.5263 (t-170) REVERT: H 31 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: H 90 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: H 188 THR cc_start: 0.5213 (OUTLIER) cc_final: 0.5005 (t) REVERT: I 138 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5004 (mt-10) REVERT: I 163 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4493 (tp30) REVERT: I 172 ASP cc_start: 0.3793 (p0) cc_final: 0.2904 (m-30) REVERT: I 230 TRP cc_start: 0.7595 (t-100) cc_final: 0.7154 (t60) REVERT: I 233 ILE cc_start: 0.7538 (pp) cc_final: 0.6960 (pt) REVERT: I 317 TRP cc_start: 0.6703 (m-90) cc_final: 0.6385 (m-90) REVERT: J 22 PHE cc_start: 0.9179 (m-80) cc_final: 0.8969 (m-80) REVERT: J 28 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5675 (tttt) REVERT: J 69 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8254 (mmpt) REVERT: J 146 TRP cc_start: 0.8040 (m-10) cc_final: 0.7772 (m-10) REVERT: J 222 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: J 330 MET cc_start: 0.6914 (mpm) cc_final: 0.6254 (ptt) outliers start: 155 outliers final: 71 residues processed: 338 average time/residue: 0.5763 time to fit residues: 236.8950 Evaluate side-chains 277 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 191 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 334 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN D 296 ASN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081969 restraints weight = 56982.607| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.39 r_work: 0.3052 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30752 Z= 0.177 Angle : 0.535 8.867 42201 Z= 0.285 Chirality : 0.041 0.321 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.645 89.483 5161 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.38 % Allowed : 29.14 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.08 (0.14), residues: 3498 helix: 1.23 (0.16), residues: 1166 sheet: 0.40 (0.22), residues: 582 loop : -1.12 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 110 TYR 0.016 0.001 TYR A 290 PHE 0.017 0.001 PHE E 302 TRP 0.011 0.001 TRP J 36 HIS 0.010 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (30752) covalent geometry : angle 0.53459 / 0.28 (42201) hydrogen bonds : bond 0.04087 / 3.78 ( 1116) hydrogen bonds : angle 4.48242 / 5.70 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 193 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: A 342 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8957 (pt) REVERT: B 47 LYS cc_start: 0.9280 (tppt) cc_final: 0.8883 (tppt) REVERT: B 55 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7919 (pp30) REVERT: B 118 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8998 (mm) REVERT: B 231 ASP cc_start: 0.7661 (p0) cc_final: 0.7423 (p0) REVERT: C 313 GLU cc_start: 0.8596 (pp20) cc_final: 0.8357 (pp20) REVERT: D 105 ASP cc_start: 0.8618 (t0) cc_final: 0.8157 (t0) REVERT: D 163 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.6664 (p0) REVERT: D 202 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: D 325 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: E 53 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8445 (p0) REVERT: E 86 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8709 (tp30) REVERT: E 287 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8361 (tm-30) REVERT: F 215 PHE cc_start: 0.8721 (m-10) cc_final: 0.8475 (m-10) REVERT: G 105 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8073 (m90) REVERT: G 260 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8772 (mtt) REVERT: G 510 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7948 (mtp180) REVERT: H 15 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5436 (ptt90) REVERT: H 29 HIS cc_start: 0.5606 (t70) cc_final: 0.4980 (t-170) REVERT: H 33 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5684 (m-10) REVERT: H 54 ARG cc_start: 0.3926 (OUTLIER) cc_final: 0.2905 (mtt-85) REVERT: H 188 THR cc_start: 0.5244 (OUTLIER) cc_final: 0.5019 (t) REVERT: I 138 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5046 (mt-10) REVERT: I 163 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.4517 (tp30) REVERT: I 172 ASP cc_start: 0.3823 (p0) cc_final: 0.2940 (m-30) REVERT: I 230 TRP cc_start: 0.7656 (t-100) cc_final: 0.7219 (t60) REVERT: I 233 ILE cc_start: 0.7539 (pp) cc_final: 0.7203 (pt) REVERT: I 283 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8157 (tp) REVERT: I 317 TRP cc_start: 0.6706 (m-90) cc_final: 0.6337 (m-90) REVERT: I 363 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5315 (tp30) REVERT: J 28 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5661 (tttt) REVERT: J 69 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8260 (mmpt) REVERT: J 146 TRP cc_start: 0.8088 (m-10) cc_final: 0.7820 (m-10) REVERT: J 222 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.4962 (m-80) REVERT: J 330 MET cc_start: 0.6990 (mpm) cc_final: 0.6341 (ptt) outliers start: 185 outliers final: 89 residues processed: 352 average time/residue: 0.5388 time to fit residues: 230.4699 Evaluate side-chains 299 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 188 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 242 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 343 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 314 optimal weight: 8.9990 chunk 330 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN H 32 ASN H 90 GLN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083107 restraints weight = 57244.258| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.39 r_work: 0.3074 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30752 Z= 0.124 Angle : 0.513 8.290 42201 Z= 0.273 Chirality : 0.040 0.238 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.646 90.149 5161 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.79 % Allowed : 29.69 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.05 (0.14), residues: 3498 helix: 1.28 (0.16), residues: 1164 sheet: 0.39 (0.22), residues: 582 loop : -1.10 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 110 TYR 0.018 0.001 TYR H 138 PHE 0.014 0.001 PHE E 302 TRP 0.010 0.001 TRP J 36 HIS 0.010 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30752) covalent geometry : angle 0.51270 / 0.27 (42201) hydrogen bonds : bond 0.03756 / 3.47 ( 1116) hydrogen bonds : angle 4.40192 / 5.58 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 197 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8777 (mt0) cc_final: 0.8473 (mt0) REVERT: A 321 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 324 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 342 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8951 (pt) REVERT: B 47 LYS cc_start: 0.9260 (tppt) cc_final: 0.8858 (tppt) REVERT: B 55 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7843 (pp30) REVERT: B 118 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8956 (mm) REVERT: C 313 GLU cc_start: 0.8587 (pp20) cc_final: 0.8358 (pp20) REVERT: D 163 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.6668 (p0) REVERT: D 202 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: D 325 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8186 (ttp) REVERT: E 53 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (p0) REVERT: E 86 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8679 (tp30) REVERT: E 287 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 215 PHE cc_start: 0.8713 (m-10) cc_final: 0.8399 (m-10) REVERT: F 286 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7822 (ttt90) REVERT: G 105 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8049 (m90) REVERT: G 260 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: G 510 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: H 15 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5359 (ptt90) REVERT: H 29 HIS cc_start: 0.5621 (t70) cc_final: 0.4894 (t-170) REVERT: H 33 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5695 (m-10) REVERT: H 54 ARG cc_start: 0.3950 (OUTLIER) cc_final: 0.2890 (mtt-85) REVERT: H 86 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4196 (mp) REVERT: H 188 THR cc_start: 0.5336 (OUTLIER) cc_final: 0.5103 (t) REVERT: I 76 THR cc_start: 0.6616 (m) cc_final: 0.6390 (p) REVERT: I 163 GLU cc_start: 0.4705 (OUTLIER) cc_final: 0.4499 (tp30) REVERT: I 172 ASP cc_start: 0.3804 (p0) cc_final: 0.2896 (m-30) REVERT: I 230 TRP cc_start: 0.7665 (t-100) cc_final: 0.7204 (t60) REVERT: I 233 ILE cc_start: 0.7560 (pp) cc_final: 0.7140 (pt) REVERT: I 283 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8148 (tp) REVERT: I 317 TRP cc_start: 0.6714 (m-90) cc_final: 0.6311 (m-90) REVERT: I 352 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7975 (mm) REVERT: I 363 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5232 (tp30) REVERT: J 69 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8222 (mmpt) REVERT: J 146 TRP cc_start: 0.8074 (m-10) cc_final: 0.7837 (m-10) REVERT: J 222 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.5000 (m-80) REVERT: J 316 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.4935 (pp) REVERT: J 330 MET cc_start: 0.7029 (mpm) cc_final: 0.6328 (ptt) outliers start: 168 outliers final: 83 residues processed: 342 average time/residue: 0.5418 time to fit residues: 225.0207 Evaluate side-chains 293 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 185 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 119 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 286 optimal weight: 0.0010 chunk 214 optimal weight: 8.9990 chunk 349 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 229 optimal weight: 1.9990 chunk 350 optimal weight: 9.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN H 90 GLN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 ASN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.127936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081120 restraints weight = 56589.517| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.32 r_work: 0.3019 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 30752 Z= 0.248 Angle : 0.588 9.660 42201 Z= 0.311 Chirality : 0.044 0.334 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.650 88.866 5160 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.76 % Allowed : 28.90 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.25 (0.14), residues: 3498 helix: 1.05 (0.16), residues: 1172 sheet: 0.29 (0.22), residues: 587 loop : -1.20 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 110 TYR 0.019 0.002 TYR A 290 PHE 0.022 0.002 PHE C 302 TRP 0.019 0.001 TRP J 381 HIS 0.007 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (30752) covalent geometry : angle 0.58780 / 0.31 (42201) hydrogen bonds : bond 0.04486 / 4.14 ( 1116) hydrogen bonds : angle 4.57169 / 5.87 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 193 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8620 (tttm) REVERT: A 324 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 342 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8979 (pt) REVERT: B 47 LYS cc_start: 0.9294 (tppt) cc_final: 0.8885 (tppt) REVERT: B 118 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8993 (mm) REVERT: C 313 GLU cc_start: 0.8630 (pp20) cc_final: 0.8425 (pp20) REVERT: D 105 ASP cc_start: 0.8633 (t0) cc_final: 0.8166 (t0) REVERT: D 202 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: E 53 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8418 (p0) REVERT: E 154 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9049 (mm) REVERT: F 28 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7659 (ttp-110) REVERT: F 215 PHE cc_start: 0.8741 (m-10) cc_final: 0.8507 (m-10) REVERT: G 80 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8257 (ptmm) REVERT: G 105 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8112 (m90) REVERT: G 260 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: G 510 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8016 (mtp180) REVERT: G 585 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7763 (tmm160) REVERT: H 29 HIS cc_start: 0.5518 (t70) cc_final: 0.5062 (t-170) REVERT: H 31 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: H 33 TYR cc_start: 0.5911 (m-10) cc_final: 0.5640 (m-10) REVERT: H 188 THR cc_start: 0.5298 (OUTLIER) cc_final: 0.5062 (t) REVERT: I 163 GLU cc_start: 0.4777 (OUTLIER) cc_final: 0.4549 (tp30) REVERT: I 172 ASP cc_start: 0.3783 (OUTLIER) cc_final: 0.2848 (m-30) REVERT: I 230 TRP cc_start: 0.7705 (t-100) cc_final: 0.7220 (t60) REVERT: I 233 ILE cc_start: 0.7611 (pp) cc_final: 0.7239 (pt) REVERT: I 283 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8172 (tp) REVERT: I 310 GLN cc_start: 0.6407 (mm110) cc_final: 0.6152 (mm-40) REVERT: I 317 TRP cc_start: 0.6746 (m-90) cc_final: 0.6342 (m-90) REVERT: I 363 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5314 (tp30) REVERT: J 146 TRP cc_start: 0.8134 (m-10) cc_final: 0.7914 (m-10) REVERT: J 222 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5165 (m-80) REVERT: J 224 TRP cc_start: 0.6504 (OUTLIER) cc_final: 0.5549 (t-100) REVERT: J 330 MET cc_start: 0.7071 (mpm) cc_final: 0.6395 (ptt) outliers start: 196 outliers final: 101 residues processed: 364 average time/residue: 0.5783 time to fit residues: 254.7686 Evaluate side-chains 307 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 185 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 585 ARG Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 90 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 213 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 243 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN H 90 GLN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN ** J 310 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 = 0.3949 r_free = 0.3949 target = 0.130342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083912 restraints weight = 56400.972| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.34 r_work: 0.3079 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30752 Z= 0.111 Angle : 0.528 8.624 42201 Z= 0.282 Chirality : 0.041 0.248 4639 Planarity : 0.004 0.060 5094 Dihedral : 14.662 90.168 5160 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.03 % Allowed : 30.93 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.09 (0.14), residues: 3498 helix: 1.24 (0.16), residues: 1163 sheet: 0.40 (0.22), residues: 572 loop : -1.13 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 110 TYR 0.026 0.001 TYR J 44 PHE 0.013 0.001 PHE E 302 TRP 0.017 0.001 TRP J 381 HIS 0.011 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (30752) covalent geometry : angle 0.52850 / 0.28 (42201) hydrogen bonds : bond 0.03689 / 3.41 ( 1116) hydrogen bonds : angle 4.41342 / 5.61 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 189 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: A 342 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8965 (pt) REVERT: B 47 LYS cc_start: 0.9241 (tppt) cc_final: 0.8834 (tppt) REVERT: B 55 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: C 313 GLU cc_start: 0.8612 (pp20) cc_final: 0.8346 (pp20) REVERT: D 163 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6722 (p0) REVERT: D 202 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: E 53 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8486 (p0) REVERT: E 86 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8734 (tp30) REVERT: E 184 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8681 (mmm-85) REVERT: F 215 PHE cc_start: 0.8701 (m-10) cc_final: 0.8491 (m-10) REVERT: F 344 GLN cc_start: 0.8039 (tt0) cc_final: 0.7808 (tt0) REVERT: G 105 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8051 (m90) REVERT: G 260 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: G 510 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7917 (mtp180) REVERT: H 29 HIS cc_start: 0.5673 (t70) cc_final: 0.5451 (t-170) REVERT: H 163 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7517 (ptp-110) REVERT: H 188 THR cc_start: 0.5383 (OUTLIER) cc_final: 0.5167 (t) REVERT: I 71 HIS cc_start: 0.5947 (m-70) cc_final: 0.5699 (m90) REVERT: I 163 GLU cc_start: 0.4772 (OUTLIER) cc_final: 0.4535 (tp30) REVERT: I 172 ASP cc_start: 0.3795 (p0) cc_final: 0.2920 (m-30) REVERT: I 230 TRP cc_start: 0.7695 (t-100) cc_final: 0.7208 (t60) REVERT: I 233 ILE cc_start: 0.7592 (pp) cc_final: 0.7232 (pt) REVERT: I 283 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (tp) REVERT: I 310 GLN cc_start: 0.6465 (mm110) cc_final: 0.6260 (mm-40) REVERT: I 317 TRP cc_start: 0.6771 (m-90) cc_final: 0.6366 (m-90) REVERT: I 328 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7240 (mpp) REVERT: I 352 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8095 (mm) REVERT: I 363 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5367 (tp30) REVERT: J 146 TRP cc_start: 0.8068 (m-10) cc_final: 0.7838 (m-10) REVERT: J 220 LEU cc_start: 0.7680 (mm) cc_final: 0.7470 (mm) REVERT: J 222 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.5106 (m-80) REVERT: J 224 TRP cc_start: 0.6474 (OUTLIER) cc_final: 0.5679 (t-100) REVERT: J 316 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.4959 (pp) REVERT: J 330 MET cc_start: 0.6931 (mpm) cc_final: 0.6043 (ptp) outliers start: 146 outliers final: 78 residues processed: 316 average time/residue: 0.5977 time to fit residues: 228.3271 Evaluate side-chains 282 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 183 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 126 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 305 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 296 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083899 restraints weight = 56996.484| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.38 r_work: 0.3092 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30752 Z= 0.112 Angle : 0.520 8.784 42201 Z= 0.277 Chirality : 0.040 0.210 4639 Planarity : 0.004 0.062 5094 Dihedral : 14.622 90.092 5160 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 5.14 % Allowed : 30.97 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.01 (0.14), residues: 3498 helix: 1.33 (0.16), residues: 1163 sheet: 0.38 (0.23), residues: 532 loop : -1.04 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.017 0.001 TYR A 290 PHE 0.013 0.001 PHE E 302 TRP 0.015 0.001 TRP J 381 HIS 0.009 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (30752) covalent geometry : angle 0.52011 / 0.28 (42201) hydrogen bonds : bond 0.03575 / 3.32 ( 1116) hydrogen bonds : angle 4.31688 / 5.50 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 193 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8783 (mt0) cc_final: 0.8478 (mt0) REVERT: A 324 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: A 342 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8957 (pt) REVERT: B 47 LYS cc_start: 0.9210 (tppt) cc_final: 0.8717 (tppt) REVERT: C 313 GLU cc_start: 0.8619 (pp20) cc_final: 0.8373 (pp20) REVERT: D 163 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.6757 (p0) REVERT: D 202 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: E 53 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8508 (p0) REVERT: E 86 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8740 (tp30) REVERT: F 215 PHE cc_start: 0.8701 (m-10) cc_final: 0.8486 (m-10) REVERT: G 105 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.8043 (m90) REVERT: G 260 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8743 (mtt) REVERT: H 29 HIS cc_start: 0.5728 (t70) cc_final: 0.5146 (t-170) REVERT: H 33 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.5662 (m-10) REVERT: H 163 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7513 (ptm160) REVERT: H 188 THR cc_start: 0.5377 (OUTLIER) cc_final: 0.5154 (t) REVERT: I 71 HIS cc_start: 0.5971 (m-70) cc_final: 0.5724 (m90) REVERT: I 163 GLU cc_start: 0.4752 (OUTLIER) cc_final: 0.4527 (tp30) REVERT: I 172 ASP cc_start: 0.3790 (OUTLIER) cc_final: 0.2904 (m-30) REVERT: I 230 TRP cc_start: 0.7739 (t-100) cc_final: 0.7238 (t60) REVERT: I 233 ILE cc_start: 0.7679 (pp) cc_final: 0.7209 (pt) REVERT: I 283 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8142 (tp) REVERT: I 310 GLN cc_start: 0.6558 (mm110) cc_final: 0.6349 (mm-40) REVERT: I 317 TRP cc_start: 0.6739 (m-90) cc_final: 0.6313 (m-90) REVERT: I 328 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: I 352 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8061 (mm) REVERT: I 363 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5332 (tp30) REVERT: J 22 PHE cc_start: 0.9168 (m-80) cc_final: 0.8963 (m-80) REVERT: J 46 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8463 (mm) REVERT: J 146 TRP cc_start: 0.8056 (m-10) cc_final: 0.7809 (m-10) REVERT: J 220 LEU cc_start: 0.7690 (mm) cc_final: 0.7483 (mm) REVERT: J 222 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.5317 (m-80) REVERT: J 224 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.5829 (t-100) REVERT: J 302 ASN cc_start: 0.4699 (OUTLIER) cc_final: 0.3405 (p0) REVERT: J 316 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.4956 (pp) REVERT: J 330 MET cc_start: 0.6809 (mpm) cc_final: 0.5956 (ptp) outliers start: 149 outliers final: 85 residues processed: 324 average time/residue: 0.5861 time to fit residues: 228.8300 Evaluate side-chains 291 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 184 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 323 optimal weight: 10.0000 chunk 352 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 355 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.130157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083102 restraints weight = 57009.911| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.37 r_work: 0.3068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30752 Z= 0.149 Angle : 0.543 9.481 42201 Z= 0.287 Chirality : 0.041 0.232 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.592 90.300 5158 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 4.72 % Allowed : 31.41 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.04 (0.14), residues: 3498 helix: 1.28 (0.16), residues: 1173 sheet: 0.38 (0.23), residues: 530 loop : -1.06 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.024 0.001 TYR F 290 PHE 0.015 0.001 PHE E 302 TRP 0.013 0.001 TRP J 381 HIS 0.009 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (30752) covalent geometry : angle 0.54300 / 0.29 (42201) hydrogen bonds : bond 0.03740 / 3.47 ( 1116) hydrogen bonds : angle 4.35810 / 5.54 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 188 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8796 (mt0) cc_final: 0.8489 (mt0) REVERT: A 321 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 324 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: A 342 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8982 (pt) REVERT: B 47 LYS cc_start: 0.9228 (tppt) cc_final: 0.8725 (tppt) REVERT: B 55 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7781 (pp30) REVERT: C 313 GLU cc_start: 0.8611 (pp20) cc_final: 0.8326 (pp20) REVERT: D 163 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6768 (p0) REVERT: D 202 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: E 53 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8519 (p0) REVERT: E 86 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8749 (tp30) REVERT: F 215 PHE cc_start: 0.8714 (m-10) cc_final: 0.8494 (m-10) REVERT: G 105 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.8060 (m90) REVERT: G 260 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8735 (mtt) REVERT: H 29 HIS cc_start: 0.5755 (t70) cc_final: 0.5157 (t-170) REVERT: H 33 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.5621 (m-10) REVERT: H 80 LYS cc_start: 0.7777 (mttt) cc_final: 0.7130 (ptpp) REVERT: H 163 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7503 (ptm160) REVERT: H 188 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5154 (t) REVERT: I 71 HIS cc_start: 0.5975 (m-70) cc_final: 0.5753 (m90) REVERT: I 72 SER cc_start: 0.2058 (OUTLIER) cc_final: 0.1808 (p) REVERT: I 172 ASP cc_start: 0.3803 (OUTLIER) cc_final: 0.2920 (m-30) REVERT: I 230 TRP cc_start: 0.7754 (t-100) cc_final: 0.7241 (t60) REVERT: I 233 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7213 (pt) REVERT: I 283 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8157 (tp) REVERT: I 308 MET cc_start: 0.7704 (ttm) cc_final: 0.7446 (ptp) REVERT: I 317 TRP cc_start: 0.6780 (m-90) cc_final: 0.6436 (m-90) REVERT: I 328 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: I 363 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5335 (tp30) REVERT: J 22 PHE cc_start: 0.9187 (m-80) cc_final: 0.8971 (m-80) REVERT: J 46 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (mm) REVERT: J 146 TRP cc_start: 0.8104 (m-10) cc_final: 0.7859 (m-10) REVERT: J 222 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: J 224 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.5686 (t-100) REVERT: J 316 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.4993 (pp) REVERT: J 330 MET cc_start: 0.6832 (mpm) cc_final: 0.5963 (ptp) outliers start: 137 outliers final: 87 residues processed: 307 average time/residue: 0.5650 time to fit residues: 210.9721 Evaluate side-chains 295 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 185 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 307 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** J 310 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 = 0.3943 r_free = 0.3943 target = 0.130149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083057 restraints weight = 56656.259| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.37 r_work: 0.3070 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30752 Z= 0.141 Angle : 0.549 10.143 42201 Z= 0.290 Chirality : 0.041 0.247 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.584 90.627 5158 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 4.10 % Allowed : 32.00 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.04 (0.14), residues: 3498 helix: 1.29 (0.16), residues: 1167 sheet: 0.44 (0.22), residues: 570 loop : -1.11 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.019 0.001 TYR A 290 PHE 0.015 0.001 PHE E 302 TRP 0.013 0.001 TRP J 381 HIS 0.009 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (30752) covalent geometry : angle 0.54891 / 0.29 (42201) hydrogen bonds : bond 0.03741 / 3.47 ( 1116) hydrogen bonds : angle 4.36340 / 5.53 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 188 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8810 (mt0) cc_final: 0.8510 (mt0) REVERT: A 324 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 342 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8986 (pt) REVERT: B 47 LYS cc_start: 0.9208 (tppt) cc_final: 0.8704 (tppt) REVERT: B 55 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7789 (pp30) REVERT: B 118 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8960 (mm) REVERT: C 313 GLU cc_start: 0.8627 (pp20) cc_final: 0.8342 (pp20) REVERT: D 163 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6798 (p0) REVERT: D 202 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: E 53 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8469 (p0) REVERT: E 86 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8736 (tp30) REVERT: F 215 PHE cc_start: 0.8713 (m-10) cc_final: 0.8491 (m-10) REVERT: G 105 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (m90) REVERT: G 260 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: H 29 HIS cc_start: 0.5767 (t70) cc_final: 0.5137 (t-170) REVERT: H 32 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.5184 (p0) REVERT: H 33 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.5650 (m-10) REVERT: H 80 LYS cc_start: 0.7812 (mttt) cc_final: 0.7183 (ptpp) REVERT: H 163 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7531 (ptm160) REVERT: H 188 THR cc_start: 0.5415 (OUTLIER) cc_final: 0.5180 (t) REVERT: I 71 HIS cc_start: 0.5963 (m-70) cc_final: 0.5720 (m90) REVERT: I 172 ASP cc_start: 0.3739 (p0) cc_final: 0.3028 (m-30) REVERT: I 230 TRP cc_start: 0.7755 (t-100) cc_final: 0.7242 (t60) REVERT: I 233 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7138 (pt) REVERT: I 283 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8173 (tp) REVERT: I 308 MET cc_start: 0.7673 (ttm) cc_final: 0.7432 (ptp) REVERT: I 317 TRP cc_start: 0.6746 (m-90) cc_final: 0.6348 (m-90) REVERT: I 328 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7152 (mpp) REVERT: I 363 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5342 (tp30) REVERT: I 384 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7913 (mm-30) REVERT: J 46 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8428 (mm) REVERT: J 54 GLN cc_start: 0.8217 (pm20) cc_final: 0.7958 (pm20) REVERT: J 146 TRP cc_start: 0.8111 (m-10) cc_final: 0.7868 (m-10) REVERT: J 222 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: J 224 TRP cc_start: 0.6606 (OUTLIER) cc_final: 0.5900 (t-100) REVERT: J 302 ASN cc_start: 0.4518 (OUTLIER) cc_final: 0.3180 (p0) REVERT: J 316 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4974 (pp) REVERT: J 330 MET cc_start: 0.6840 (mpm) cc_final: 0.5934 (ptp) outliers start: 119 outliers final: 83 residues processed: 291 average time/residue: 0.5865 time to fit residues: 207.5838 Evaluate side-chains 289 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 183 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 119 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 120 optimal weight: 0.0570 chunk 246 optimal weight: 0.5980 chunk 302 optimal weight: 40.0000 chunk 164 optimal weight: 0.3980 chunk 177 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084108 restraints weight = 56668.782| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.32 r_work: 0.3085 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.348 30752 Z= 0.220 Angle : 0.731 59.191 42201 Z= 0.447 Chirality : 0.045 1.290 4639 Planarity : 0.005 0.170 5094 Dihedral : 14.581 90.625 5157 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 4.07 % Allowed : 32.03 % Favored : 63.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.35 % 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 are not related in a simple way. whole: -0.04 (0.14), residues: 3498 helix: 1.28 (0.16), residues: 1167 sheet: 0.44 (0.22), residues: 570 loop : -1.11 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 110 TYR 0.019 0.001 TYR A 290 PHE 0.015 0.001 PHE E 302 TRP 0.014 0.001 TRP J 224 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (30752) covalent geometry : angle 0.73077 / 0.45 (42201) hydrogen bonds : bond 0.03717 / 3.44 ( 1116) hydrogen bonds : angle 4.35785 / 5.50 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14768.99 seconds wall clock time: 251 minutes 29.32 seconds (15089.32 seconds total)