Starting phenix.real_space_refine on Fri Mar 6 11:36:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtp_65338/03_2026/9vtp_65338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtp_65338/03_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_65338/03_2026/9vtp_65338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtp_65338/03_2026/9vtp_65338.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtp_65338/03_2026/9vtp_65338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtp_65338/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.44, per 1000 atoms: 0.22 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 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: 4.16 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: 6.90 Time building geometry restraints manager: 3.55 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=" CB GLU E 287 " pdb=" CG GLU E 287 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CA PRO J 107 " pdb=" CB PRO J 107 " ideal model delta sigma weight residual 1.531 1.523 0.008 6.20e-03 2.60e+04 1.59e+00 bond pdb=" CG LEU J 305 " pdb=" CD1 LEU J 305 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.57e+00 bond pdb=" CB ASP J 158 " pdb=" CG ASP J 158 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.47e+00 bond pdb=" CB GLU G 268 " pdb=" CG GLU G 268 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 ... (remaining 30747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 41632 2.08 - 4.16: 490 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=" CA LYS J 306 " pdb=" CB LYS J 306 " pdb=" CG LYS J 306 " ideal model delta sigma weight residual 114.10 122.13 -8.03 2.00e+00 2.50e-01 1.61e+01 angle pdb=" N LYS I 70 " pdb=" CA LYS I 70 " pdb=" C LYS I 70 " ideal model delta sigma weight residual 113.43 108.94 4.49 1.26e+00 6.30e-01 1.27e+01 angle pdb=" N GLY I 209 " pdb=" CA GLY I 209 " pdb=" C GLY I 209 " ideal model delta sigma weight residual 113.18 121.09 -7.91 2.37e+00 1.78e-01 1.11e+01 angle pdb=" CA TYR G 176 " pdb=" CB TYR G 176 " pdb=" CG TYR G 176 " ideal model delta sigma weight residual 113.90 119.66 -5.76 1.80e+00 3.09e-01 1.02e+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: 4060 0.059 - 0.119: 539 0.119 - 0.178: 39 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=" CA ASP J 158 " pdb=" N ASP J 158 " pdb=" C ASP J 158 " pdb=" CB ASP J 158 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-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: 9.310 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: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.820 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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= 0.126 Angle : 0.573 10.406 42201 Z= 0.300 Chirality : 0.041 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 covalent geometry : bond 0.00272 (30752) covalent geometry : angle 0.57276 (42201) hydrogen bonds : bond 0.13207 ( 1116) hydrogen bonds : angle 5.43401 ( 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 : 1.096 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: 0.5718 time to fit residues: 188.6490 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 : 1.116 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3922 r_free = 0.3922 target = 0.128402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081474 restraints weight = 56632.303| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.35 r_work: 0.3030 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30752 Z= 0.197 Angle : 0.558 7.598 42201 Z= 0.293 Chirality : 0.042 0.244 4639 Planarity : 0.004 0.058 5094 Dihedral : 14.886 88.725 5222 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.69 % Allowed : 28.03 % Favored : 65.28 % 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: -0.19 (0.14), residues: 3498 helix: 1.14 (0.16), residues: 1153 sheet: 0.34 (0.22), residues: 590 loop : -1.17 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 121 TYR 0.017 0.001 TYR G 420 PHE 0.020 0.001 PHE E 302 TRP 0.012 0.001 TRP J 381 HIS 0.013 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00449 (30752) covalent geometry : angle 0.55764 (42201) hydrogen bonds : bond 0.04332 ( 1116) hydrogen bonds : angle 4.63702 ( 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 393 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 199 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 109 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8594 (tttm) REVERT: A 324 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 342 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8931 (pt) REVERT: B 47 LYS cc_start: 0.9282 (tppt) cc_final: 0.8873 (tppt) REVERT: B 55 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7845 (pp30) REVERT: B 118 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9010 (mm) REVERT: B 185 ASP cc_start: 0.8815 (m-30) cc_final: 0.8597 (m-30) REVERT: B 231 ASP cc_start: 0.7614 (p0) cc_final: 0.7350 (p0) REVERT: C 313 GLU cc_start: 0.8849 (pp20) cc_final: 0.8491 (pp20) REVERT: D 105 ASP cc_start: 0.8684 (t0) cc_final: 0.8135 (t0) REVERT: D 202 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7049 (mp10) REVERT: E 53 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8525 (p0) REVERT: F 215 PHE cc_start: 0.8760 (m-10) cc_final: 0.8546 (m-10) REVERT: F 314 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: F 344 GLN cc_start: 0.8081 (tt0) cc_final: 0.7873 (tt0) REVERT: G 80 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8257 (ptmm) REVERT: G 105 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.8080 (m90) REVERT: G 260 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8764 (mtt) REVERT: G 510 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7999 (mtp180) REVERT: G 585 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7717 (tmm160) REVERT: H 29 HIS cc_start: 0.5671 (t70) cc_final: 0.5277 (t-170) REVERT: H 32 ASN cc_start: 0.5538 (OUTLIER) cc_final: 0.5326 (p0) REVERT: H 188 THR cc_start: 0.5205 (OUTLIER) cc_final: 0.4996 (t) REVERT: I 138 GLU cc_start: 0.5883 (tm-30) cc_final: 0.5027 (mt-10) REVERT: I 163 GLU cc_start: 0.4714 (OUTLIER) cc_final: 0.4511 (tp30) REVERT: I 172 ASP cc_start: 0.3626 (p0) cc_final: 0.2784 (m-30) REVERT: I 233 ILE cc_start: 0.7549 (pp) cc_final: 0.7276 (pt) REVERT: I 283 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8159 (tp) REVERT: I 317 TRP cc_start: 0.6719 (m-90) cc_final: 0.6357 (m-90) REVERT: J 28 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5660 (tttt) REVERT: J 69 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8334 (mmpt) REVERT: J 146 TRP cc_start: 0.8081 (m-10) cc_final: 0.7822 (m-10) REVERT: J 222 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: J 330 MET cc_start: 0.6956 (mpm) cc_final: 0.6289 (ptt) outliers start: 194 outliers final: 82 residues processed: 369 average time/residue: 0.5736 time to fit residues: 255.3085 Evaluate side-chains 286 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 185 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 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 59 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU 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 60 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 289 VAL 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 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 315 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 118 LEU 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 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 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 314 GLN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 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 585 ARG Chi-restraints excluded: chain G residue 598 THR 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 108 ASP 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 132 CYS Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 283 ILE 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 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 181 VAL 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 Chi-restraints excluded: chain J residue 396 LEU 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: 0.8980 chunk 148 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 218 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.130162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082960 restraints weight = 57367.773| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.39 r_work: 0.3072 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0708 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= 0.127 Angle : 0.517 7.309 42201 Z= 0.270 Chirality : 0.040 0.163 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.768 89.352 5183 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.55 % Allowed : 29.76 % Favored : 64.69 % 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: 1.27 (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 0.008 0.000 ARG D 110 TYR 0.016 0.001 TYR E 52 PHE 0.014 0.001 PHE E 302 TRP 0.014 0.001 TRP J 381 HIS 0.012 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00285 (30752) covalent geometry : angle 0.51663 (42201) hydrogen bonds : bond 0.03667 ( 1116) hydrogen bonds : angle 4.43472 ( 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 363 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 202 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8719 (tptp) REVERT: A 321 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 342 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8934 (pt) REVERT: B 47 LYS cc_start: 0.9265 (tppt) cc_final: 0.8865 (tppt) REVERT: B 55 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7879 (pp30) REVERT: C 313 GLU cc_start: 0.8845 (pp20) cc_final: 0.8502 (pp20) REVERT: D 105 ASP cc_start: 0.8586 (t0) cc_final: 0.8002 (t0) REVERT: D 163 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6634 (p0) REVERT: E 53 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8481 (p0) REVERT: E 86 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8741 (tp30) REVERT: E 287 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 215 PHE cc_start: 0.8712 (m-10) cc_final: 0.8488 (m-10) REVERT: F 314 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: G 105 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8065 (m90) REVERT: G 260 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8748 (mtt) REVERT: H 29 HIS cc_start: 0.5652 (t70) cc_final: 0.5158 (t-170) REVERT: H 32 ASN cc_start: 0.5541 (OUTLIER) cc_final: 0.5165 (p0) REVERT: H 33 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.5731 (m-10) REVERT: H 188 THR cc_start: 0.5323 (OUTLIER) cc_final: 0.5092 (t) REVERT: I 163 GLU cc_start: 0.4708 (OUTLIER) cc_final: 0.4490 (tp30) REVERT: I 172 ASP cc_start: 0.3649 (p0) cc_final: 0.2788 (m-30) REVERT: I 230 TRP cc_start: 0.7678 (t-100) cc_final: 0.7215 (t60) REVERT: I 233 ILE cc_start: 0.7588 (pp) cc_final: 0.7189 (pt) REVERT: I 283 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8133 (tp) REVERT: I 317 TRP cc_start: 0.6734 (m-90) cc_final: 0.6405 (m-90) REVERT: I 363 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5316 (tp30) REVERT: J 69 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8232 (mmpt) REVERT: J 146 TRP cc_start: 0.8099 (m-10) cc_final: 0.7856 (m-10) REVERT: J 222 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: J 330 MET cc_start: 0.7024 (mpm) cc_final: 0.6322 (ptt) outliers start: 161 outliers final: 65 residues processed: 341 average time/residue: 0.5664 time to fit residues: 232.9068 Evaluate side-chains 271 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 189 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain A residue 230 LYS 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 55 GLN 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 301 LEU 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 289 VAL 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 324 GLU 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 116 ILE Chi-restraints excluded: chain E residue 228 VAL 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 219 THR Chi-restraints excluded: chain F residue 228 VAL 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 F residue 314 GLN 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 239 THR 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 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 598 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 54 ARG Chi-restraints excluded: chain H residue 57 THR 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 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 283 ILE 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 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: 5.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 221 optimal weight: 0.0370 chunk 326 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 296 ASN I 310 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 = 0.3955 r_free = 0.3955 target = 0.130916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083925 restraints weight = 57040.614| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.39 r_work: 0.3091 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: 0.8674 moved from start: 0.0883 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= 0.112 Angle : 0.502 8.019 42201 Z= 0.262 Chirality : 0.040 0.164 4639 Planarity : 0.004 0.062 5094 Dihedral : 14.638 90.616 5170 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.79 % Allowed : 29.86 % 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: 0.05 (0.14), residues: 3498 helix: 1.37 (0.16), residues: 1163 sheet: 0.48 (0.22), residues: 570 loop : -1.06 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 110 TYR 0.014 0.001 TYR G 420 PHE 0.013 0.001 PHE E 302 TRP 0.012 0.001 TRP J 36 HIS 0.010 0.000 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00251 (30752) covalent geometry : angle 0.50191 (42201) hydrogen bonds : bond 0.03407 ( 1116) hydrogen bonds : angle 4.29046 ( 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 375 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 207 time to evaluate : 1.186 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: 0.8749 (mt0) cc_final: 0.8437 (mt0) REVERT: A 342 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8966 (pt) REVERT: B 47 LYS cc_start: 0.9240 (tppt) cc_final: 0.8832 (tppt) REVERT: B 55 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7827 (pp30) REVERT: B 231 ASP cc_start: 0.7634 (p0) cc_final: 0.7412 (p0) REVERT: C 313 GLU cc_start: 0.8828 (pp20) cc_final: 0.8482 (pp20) REVERT: D 163 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6721 (p0) REVERT: D 202 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: E 86 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8740 (tp30) REVERT: E 287 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8352 (tm-30) REVERT: E 325 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8536 (tmm) REVERT: F 215 PHE cc_start: 0.8703 (m-10) cc_final: 0.8482 (m-10) REVERT: F 314 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: G 105 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.8030 (m90) REVERT: G 260 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8752 (mtt) REVERT: G 510 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7906 (mtp180) REVERT: H 29 HIS cc_start: 0.5660 (t70) cc_final: 0.5046 (t-170) REVERT: H 32 ASN cc_start: 0.5481 (OUTLIER) cc_final: 0.5074 (p0) REVERT: H 33 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5684 (m-10) REVERT: H 188 THR cc_start: 0.5374 (OUTLIER) cc_final: 0.5154 (t) REVERT: I 71 HIS cc_start: 0.5950 (m-70) cc_final: 0.5710 (m90) REVERT: I 76 THR cc_start: 0.6458 (m) cc_final: 0.6245 (p) REVERT: I 104 GLN cc_start: 0.5230 (tp40) cc_final: 0.5002 (tp40) REVERT: I 163 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4518 (tp30) REVERT: I 172 ASP cc_start: 0.3801 (p0) cc_final: 0.2940 (m-30) REVERT: I 230 TRP cc_start: 0.7710 (t-100) cc_final: 0.7227 (t60) REVERT: I 233 ILE cc_start: 0.7575 (pp) cc_final: 0.7173 (pt) REVERT: I 317 TRP cc_start: 0.6718 (m-90) cc_final: 0.6361 (m-90) REVERT: I 328 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7174 (mpp) REVERT: I 363 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5372 (tp30) REVERT: J 46 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (mm) REVERT: J 146 TRP cc_start: 0.8068 (m-10) cc_final: 0.7824 (m-10) REVERT: J 222 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.4963 (m-80) REVERT: J 308 MET cc_start: 0.7038 (ppp) cc_final: 0.6808 (ppp) REVERT: J 330 MET cc_start: 0.7148 (mpm) cc_final: 0.6404 (ptt) REVERT: J 333 ILE cc_start: 0.7769 (pt) cc_final: 0.7227 (tp) outliers start: 168 outliers final: 75 residues processed: 349 average time/residue: 0.5692 time to fit residues: 238.8844 Evaluate side-chains 285 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 192 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 323 ASP 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 92 SER 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 301 LEU 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 164 GLU Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL 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 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 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 MET 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 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 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 239 THR 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 559 ILE 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 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 THR 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 155 HIS Chi-restraints excluded: chain I residue 163 GLU 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 31 TYR Chi-restraints excluded: chain J residue 46 LEU 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 373 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 242 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 343 optimal weight: 30.0000 chunk 57 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 231 optimal weight: 0.1980 chunk 314 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.130805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083773 restraints weight = 57206.009| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.39 r_work: 0.3090 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1012 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= 0.118 Angle : 0.506 7.662 42201 Z= 0.263 Chirality : 0.040 0.163 4639 Planarity : 0.004 0.058 5094 Dihedral : 14.588 91.330 5165 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.93 % Allowed : 29.69 % Favored : 64.38 % 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: 1.45 (0.16), residues: 1161 sheet: 0.52 (0.22), residues: 572 loop : -1.06 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 110 TYR 0.015 0.001 TYR A 290 PHE 0.046 0.001 PHE J 309 TRP 0.017 0.001 TRP J 381 HIS 0.009 0.000 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00265 (30752) covalent geometry : angle 0.50553 (42201) hydrogen bonds : bond 0.03414 ( 1116) hydrogen bonds : angle 4.26903 ( 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 374 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 202 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8754 (mt0) cc_final: 0.8446 (mt0) REVERT: A 109 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8548 (tttm) REVERT: A 324 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: A 342 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8957 (pt) REVERT: B 47 LYS cc_start: 0.9197 (tppt) cc_final: 0.8688 (tppt) REVERT: B 55 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7873 (pp30) REVERT: C 313 GLU cc_start: 0.8817 (pp20) cc_final: 0.8476 (pp20) REVERT: D 163 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.6776 (p0) REVERT: D 202 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: E 86 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8727 (tp30) REVERT: E 287 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8396 (tm-30) REVERT: F 215 PHE cc_start: 0.8697 (m-10) cc_final: 0.8478 (m-10) REVERT: F 314 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: G 105 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.8031 (m90) REVERT: G 260 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8738 (mtt) REVERT: G 510 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7922 (mtp180) REVERT: H 29 HIS cc_start: 0.5751 (t70) cc_final: 0.5140 (t-170) REVERT: H 32 ASN cc_start: 0.5473 (OUTLIER) cc_final: 0.4995 (p0) REVERT: H 33 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.5708 (m-10) REVERT: H 163 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7534 (ptm160) REVERT: H 188 THR cc_start: 0.5390 (OUTLIER) cc_final: 0.5161 (t) REVERT: I 71 HIS cc_start: 0.5998 (m-70) cc_final: 0.5747 (m90) REVERT: I 76 THR cc_start: 0.6383 (m) cc_final: 0.6175 (p) REVERT: I 163 GLU cc_start: 0.4740 (OUTLIER) cc_final: 0.4514 (tp30) REVERT: I 172 ASP cc_start: 0.3758 (p0) cc_final: 0.2946 (m-30) REVERT: I 230 TRP cc_start: 0.7782 (t-100) cc_final: 0.7285 (t60) REVERT: I 233 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7214 (pt) REVERT: I 317 TRP cc_start: 0.6737 (m-90) cc_final: 0.6324 (m-90) REVERT: I 323 LEU cc_start: 0.8713 (mp) cc_final: 0.8267 (tp) REVERT: I 328 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7094 (mpp) REVERT: I 363 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5358 (tp30) REVERT: J 46 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8300 (mm) REVERT: J 146 TRP cc_start: 0.8100 (m-10) cc_final: 0.7852 (m-10) REVERT: J 222 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: J 330 MET cc_start: 0.7179 (mpm) cc_final: 0.6445 (ptt) REVERT: J 333 ILE cc_start: 0.7790 (pt) cc_final: 0.7323 (tp) outliers start: 172 outliers final: 91 residues processed: 346 average time/residue: 0.5732 time to fit residues: 238.3400 Evaluate side-chains 304 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 192 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS 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 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 301 LEU 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 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 116 ILE 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 344 GLN Chi-restraints excluded: chain E residue 10 MET 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 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 20 PHE 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 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 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 239 THR 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 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 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 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 233 ILE 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 31 TYR Chi-restraints excluded: chain J residue 46 LEU 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 336 LEU Chi-restraints excluded: chain J residue 373 TYR 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: 10.0000 chunk 222 optimal weight: 7.9990 chunk 232 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 349 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 229 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080898 restraints weight = 56886.118| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.39 r_work: 0.3030 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30752 Z= 0.196 Angle : 0.557 8.757 42201 Z= 0.290 Chirality : 0.042 0.162 4639 Planarity : 0.004 0.058 5094 Dihedral : 14.602 90.086 5165 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.31 % Allowed : 29.62 % Favored : 64.07 % 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: 1.27 (0.16), residues: 1174 sheet: 0.45 (0.22), residues: 580 loop : -1.12 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 110 TYR 0.018 0.001 TYR A 290 PHE 0.035 0.002 PHE J 309 TRP 0.018 0.001 TRP J 381 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00450 (30752) covalent geometry : angle 0.55702 (42201) hydrogen bonds : bond 0.03984 ( 1116) hydrogen bonds : angle 4.41036 ( 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 379 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 196 time to evaluate : 1.162 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 109 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8585 (tttm) REVERT: A 122 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8471 (mtpp) REVERT: A 324 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: A 342 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9007 (pt) REVERT: B 47 LYS cc_start: 0.9227 (tppt) cc_final: 0.8722 (tppt) REVERT: B 118 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 185 ASP cc_start: 0.8805 (m-30) cc_final: 0.8601 (m-30) REVERT: C 313 GLU cc_start: 0.8867 (pp20) cc_final: 0.8528 (pp20) REVERT: D 163 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6671 (p0) REVERT: D 202 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: F 28 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7654 (ttp-110) REVERT: F 215 PHE cc_start: 0.8716 (m-10) cc_final: 0.8480 (m-10) REVERT: F 231 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7889 (t70) REVERT: F 314 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: G 105 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8105 (m90) REVERT: G 260 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8749 (mtt) REVERT: G 510 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: H 29 HIS cc_start: 0.5882 (t70) cc_final: 0.5466 (t-170) REVERT: H 33 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5688 (m-10) REVERT: H 80 LYS cc_start: 0.7710 (mttt) cc_final: 0.7070 (ptpp) REVERT: H 188 THR cc_start: 0.5418 (OUTLIER) cc_final: 0.5169 (t) REVERT: I 71 HIS cc_start: 0.5983 (m-70) cc_final: 0.5720 (m90) REVERT: I 163 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4576 (tp30) REVERT: I 172 ASP cc_start: 0.3774 (OUTLIER) cc_final: 0.2924 (m-30) REVERT: I 230 TRP cc_start: 0.7822 (t-100) cc_final: 0.7331 (t60) REVERT: I 233 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7203 (pt) REVERT: I 317 TRP cc_start: 0.6756 (m-90) cc_final: 0.6362 (m-90) REVERT: I 323 LEU cc_start: 0.8759 (mp) cc_final: 0.8280 (tp) REVERT: I 328 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: I 363 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5276 (tp30) REVERT: J 46 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8275 (mm) REVERT: J 69 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8130 (mmpt) REVERT: J 146 TRP cc_start: 0.8190 (m-10) cc_final: 0.7968 (m-10) REVERT: J 222 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5142 (m-80) REVERT: J 316 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.4958 (pp) REVERT: J 330 MET cc_start: 0.7252 (mpm) cc_final: 0.6494 (ptt) REVERT: J 333 ILE cc_start: 0.7817 (pt) cc_final: 0.7375 (tp) outliers start: 183 outliers final: 98 residues processed: 354 average time/residue: 0.5660 time to fit residues: 240.7208 Evaluate side-chains 311 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 189 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 122 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 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 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 B residue 301 LEU 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 148 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 116 ILE 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 324 GLU 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 180 THR Chi-restraints excluded: chain E residue 280 SER 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 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 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 473 THR 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 559 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 572 CYS Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 54 ARG 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 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 233 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 69 LYS 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 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: 0.7980 chunk 251 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 84 GLN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081649 restraints weight = 56851.943| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.40 r_work: 0.3044 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30752 Z= 0.162 Angle : 0.546 8.638 42201 Z= 0.283 Chirality : 0.041 0.164 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.596 89.680 5161 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.55 % Allowed : 30.48 % Favored : 63.97 % 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: -0.06 (0.14), residues: 3498 helix: 1.30 (0.16), residues: 1160 sheet: 0.43 (0.22), residues: 570 loop : -1.14 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 110 TYR 0.018 0.001 TYR A 290 PHE 0.032 0.001 PHE J 309 TRP 0.016 0.001 TRP J 381 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00370 (30752) covalent geometry : angle 0.54592 (42201) hydrogen bonds : bond 0.03780 ( 1116) hydrogen bonds : angle 4.36877 ( 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 358 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 197 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8577 (tttm) REVERT: A 122 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8438 (mtpp) REVERT: A 321 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 324 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 342 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8991 (pt) REVERT: B 47 LYS cc_start: 0.9208 (tppt) cc_final: 0.8700 (tppt) REVERT: B 118 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8965 (mm) REVERT: B 231 ASP cc_start: 0.7606 (p0) cc_final: 0.7388 (p0) REVERT: C 313 GLU cc_start: 0.8851 (pp20) cc_final: 0.8512 (pp20) REVERT: D 163 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.6700 (p0) REVERT: D 202 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: F 215 PHE cc_start: 0.8712 (m-10) cc_final: 0.8505 (m-10) REVERT: F 231 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7828 (t70) REVERT: F 314 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: G 105 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8075 (m90) REVERT: G 260 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8752 (mtt) REVERT: G 510 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7993 (mtp180) REVERT: H 29 HIS cc_start: 0.6183 (t70) cc_final: 0.5946 (t-170) REVERT: H 80 LYS cc_start: 0.7710 (mttt) cc_final: 0.7077 (ptpp) REVERT: H 163 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: H 188 THR cc_start: 0.5327 (OUTLIER) cc_final: 0.5085 (t) REVERT: I 71 HIS cc_start: 0.6003 (m-70) cc_final: 0.5736 (m90) REVERT: I 138 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5093 (mp0) REVERT: I 163 GLU cc_start: 0.4801 (OUTLIER) cc_final: 0.4585 (tp30) REVERT: I 172 ASP cc_start: 0.3781 (p0) cc_final: 0.2931 (m-30) REVERT: I 230 TRP cc_start: 0.7825 (t-100) cc_final: 0.7343 (t60) REVERT: I 233 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7204 (pt) REVERT: I 317 TRP cc_start: 0.6736 (m-90) cc_final: 0.6273 (m-90) REVERT: I 323 LEU cc_start: 0.8751 (mp) cc_final: 0.8257 (tp) REVERT: I 328 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7262 (mpp) REVERT: I 363 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5333 (tp30) REVERT: J 46 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8259 (mm) REVERT: J 146 TRP cc_start: 0.8175 (m-10) cc_final: 0.7953 (m-10) REVERT: J 222 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: J 316 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.4984 (pp) REVERT: J 330 MET cc_start: 0.7258 (mpm) cc_final: 0.6498 (ptt) REVERT: J 333 ILE cc_start: 0.7817 (pt) cc_final: 0.7386 (tp) outliers start: 161 outliers final: 87 residues processed: 338 average time/residue: 0.5869 time to fit residues: 237.2062 Evaluate side-chains 298 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 188 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 122 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 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 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 301 LEU 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 289 VAL 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 310 GLN Chi-restraints excluded: chain E residue 64 SER 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 123 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 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 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 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 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR 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 138 GLU Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET 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 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 Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 126 optimal weight: 0.4980 chunk 224 optimal weight: 30.0000 chunk 137 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 296 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 84 GLN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081170 restraints weight = 56911.906| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.40 r_work: 0.3032 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30752 Z= 0.184 Angle : 0.565 10.367 42201 Z= 0.293 Chirality : 0.042 0.168 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.587 89.412 5158 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.28 % Allowed : 30.76 % Favored : 63.97 % 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: 1.23 (0.16), residues: 1160 sheet: 0.41 (0.22), residues: 575 loop : -1.14 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 121 TYR 0.019 0.001 TYR A 290 PHE 0.029 0.001 PHE J 309 TRP 0.015 0.001 TRP J 381 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00421 (30752) covalent geometry : angle 0.56491 (42201) hydrogen bonds : bond 0.03948 ( 1116) hydrogen bonds : angle 4.40765 ( 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 351 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 198 time to evaluate : 1.184 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: 0.8969 (OUTLIER) cc_final: 0.8594 (tttm) REVERT: A 122 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8442 (mtpp) REVERT: A 324 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: A 342 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9004 (pt) REVERT: B 47 LYS cc_start: 0.9209 (tppt) cc_final: 0.8709 (tppt) REVERT: B 118 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8978 (mm) REVERT: C 313 GLU cc_start: 0.8859 (pp20) cc_final: 0.8515 (pp20) REVERT: D 163 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.6627 (p0) REVERT: D 202 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.6969 (mp10) REVERT: E 287 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8396 (tm-30) REVERT: F 28 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7602 (ttp-110) REVERT: F 148 CYS cc_start: 0.8528 (t) cc_final: 0.8151 (p) REVERT: F 215 PHE cc_start: 0.8733 (m-10) cc_final: 0.8515 (m-10) REVERT: F 231 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (t70) REVERT: F 314 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: G 105 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8101 (m90) REVERT: G 260 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8754 (mtt) REVERT: G 510 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: G 585 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7749 (tmm160) REVERT: H 80 LYS cc_start: 0.7733 (mttt) cc_final: 0.7104 (ptpp) REVERT: H 188 THR cc_start: 0.5386 (OUTLIER) cc_final: 0.5133 (t) REVERT: I 71 HIS cc_start: 0.5997 (m-70) cc_final: 0.5733 (m90) REVERT: I 121 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6493 (ttt-90) REVERT: I 138 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5050 (mp0) REVERT: I 172 ASP cc_start: 0.3780 (OUTLIER) cc_final: 0.2918 (m-30) REVERT: I 230 TRP cc_start: 0.7838 (t-100) cc_final: 0.7340 (t60) REVERT: I 233 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7204 (pt) REVERT: I 308 MET cc_start: 0.7608 (ttm) cc_final: 0.7383 (ptp) REVERT: I 317 TRP cc_start: 0.6726 (m-90) cc_final: 0.6285 (m-90) REVERT: I 323 LEU cc_start: 0.8757 (mp) cc_final: 0.8273 (tp) REVERT: I 328 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: I 363 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.5253 (tp30) REVERT: J 46 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8248 (mm) REVERT: J 146 TRP cc_start: 0.8204 (m-10) cc_final: 0.8000 (m-10) REVERT: J 316 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5057 (pp) REVERT: J 330 MET cc_start: 0.7334 (mpm) cc_final: 0.6593 (ptt) REVERT: J 333 ILE cc_start: 0.7906 (pt) cc_final: 0.7482 (tp) outliers start: 153 outliers final: 97 residues processed: 335 average time/residue: 0.6044 time to fit residues: 241.2743 Evaluate side-chains 309 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 189 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 122 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 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 91 VAL Chi-restraints excluded: chain B residue 92 SER 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 301 LEU 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 148 CYS Chi-restraints excluded: chain C residue 289 VAL 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 64 SER 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 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 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 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 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 20 ILE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL 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 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 121 ARG 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 158 ASP 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 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 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 Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 373 TYR 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: 6.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 258 optimal weight: 0.0670 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 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** J 84 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.129648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082104 restraints weight = 56916.535| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.42 r_work: 0.3060 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1192 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= 0.147 Angle : 0.553 9.762 42201 Z= 0.287 Chirality : 0.041 0.162 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.559 89.614 5158 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.86 % Allowed : 31.31 % Favored : 63.83 % 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: -0.03 (0.14), residues: 3498 helix: 1.32 (0.16), residues: 1156 sheet: 0.45 (0.22), residues: 570 loop : -1.11 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 110 TYR 0.018 0.001 TYR A 290 PHE 0.029 0.001 PHE J 309 TRP 0.015 0.001 TRP J 381 HIS 0.006 0.001 HIS I 228 Details of bonding type rmsd covalent geometry : bond 0.00335 (30752) covalent geometry : angle 0.55336 (42201) hydrogen bonds : bond 0.03699 ( 1116) hydrogen bonds : angle 4.35582 ( 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 334 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 193 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8597 (tttm) REVERT: A 118 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 122 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: A 324 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 342 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8991 (pt) REVERT: B 47 LYS cc_start: 0.9212 (tppt) cc_final: 0.8717 (tppt) REVERT: B 118 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 185 ASP cc_start: 0.8814 (m-30) cc_final: 0.8588 (p0) REVERT: C 313 GLU cc_start: 0.8835 (pp20) cc_final: 0.8501 (pp20) REVERT: D 163 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6702 (p0) REVERT: D 202 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: F 28 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7604 (ttp-110) REVERT: F 215 PHE cc_start: 0.8701 (m-10) cc_final: 0.8468 (m-10) REVERT: F 231 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7832 (t70) REVERT: F 314 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: G 105 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8072 (m90) REVERT: G 260 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8746 (mtt) REVERT: G 510 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7956 (mtp180) REVERT: G 585 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7784 (tmm160) REVERT: H 80 LYS cc_start: 0.7699 (mttt) cc_final: 0.7083 (ptpp) REVERT: H 188 THR cc_start: 0.5424 (OUTLIER) cc_final: 0.5158 (t) REVERT: I 71 HIS cc_start: 0.6005 (m-70) cc_final: 0.5737 (m90) REVERT: I 121 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6474 (ttt-90) REVERT: I 138 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: I 172 ASP cc_start: 0.3644 (p0) cc_final: 0.2893 (m-30) REVERT: I 230 TRP cc_start: 0.7861 (t-100) cc_final: 0.7368 (t60) REVERT: I 233 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7158 (pt) REVERT: I 308 MET cc_start: 0.7615 (ttm) cc_final: 0.7396 (ptp) REVERT: I 317 TRP cc_start: 0.6737 (m-90) cc_final: 0.6289 (m-90) REVERT: I 323 LEU cc_start: 0.8764 (mp) cc_final: 0.8289 (tp) REVERT: I 328 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7341 (mpp) REVERT: I 363 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.5094 (tp30) REVERT: J 42 LYS cc_start: 0.8687 (tptm) cc_final: 0.8433 (tptm) REVERT: J 46 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8213 (mm) REVERT: J 146 TRP cc_start: 0.8173 (m-10) cc_final: 0.7945 (m-10) REVERT: J 316 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5134 (pp) REVERT: J 330 MET cc_start: 0.7322 (mpm) cc_final: 0.6600 (ptt) REVERT: J 333 ILE cc_start: 0.7912 (pt) cc_final: 0.7504 (tp) outliers start: 141 outliers final: 93 residues processed: 319 average time/residue: 0.5759 time to fit residues: 220.9529 Evaluate side-chains 302 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 186 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 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 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 91 VAL Chi-restraints excluded: chain B residue 92 SER 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 301 LEU 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 148 CYS Chi-restraints excluded: chain C residue 289 VAL 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 324 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 64 SER 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 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 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 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET 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 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 20 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 142 THR 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 121 ARG 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 233 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET 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 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 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 307 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 258 optimal weight: 0.4980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** J 84 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.131052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083922 restraints weight = 56662.166| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.39 r_work: 0.3096 rms_B_bonded: 2.96 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: 0.8675 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30752 Z= 0.118 Angle : 0.542 11.324 42201 Z= 0.280 Chirality : 0.040 0.163 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.525 90.822 5158 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.76 % Allowed : 32.41 % Favored : 63.83 % 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: 0.07 (0.14), residues: 3498 helix: 1.41 (0.16), residues: 1160 sheet: 0.49 (0.22), residues: 582 loop : -1.06 (0.15), residues: 1756 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 0.029 0.001 PHE J 309 TRP 0.016 0.001 TRP J 381 HIS 0.007 0.000 HIS I 228 Details of bonding type rmsd covalent geometry : bond 0.00266 (30752) covalent geometry : angle 0.54186 (42201) hydrogen bonds : bond 0.03425 ( 1116) hydrogen bonds : angle 4.23970 ( 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: 109 poor density : 198 time to evaluate : 1.088 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: 0.8763 (mt0) cc_final: 0.8464 (mt0) REVERT: A 118 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9054 (mm) REVERT: A 122 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: A 324 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 342 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8989 (pt) REVERT: B 47 LYS cc_start: 0.9188 (tppt) cc_final: 0.8684 (tppt) REVERT: B 118 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8939 (mm) REVERT: C 313 GLU cc_start: 0.8826 (pp20) cc_final: 0.8450 (pp20) REVERT: D 163 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.6765 (p0) REVERT: D 202 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6660 (mp10) REVERT: F 28 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7567 (ttp-110) REVERT: F 148 CYS cc_start: 0.8468 (t) cc_final: 0.8061 (p) REVERT: F 215 PHE cc_start: 0.8696 (m-10) cc_final: 0.8478 (m-10) REVERT: F 231 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7830 (t70) REVERT: G 105 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8034 (m90) REVERT: G 260 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8726 (mtt) REVERT: G 510 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7916 (mtp180) REVERT: H 188 THR cc_start: 0.5426 (OUTLIER) cc_final: 0.5159 (t) REVERT: I 71 HIS cc_start: 0.5994 (m-70) cc_final: 0.5737 (m90) REVERT: I 76 THR cc_start: 0.6602 (m) cc_final: 0.6383 (p) REVERT: I 121 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6447 (ttt-90) REVERT: I 172 ASP cc_start: 0.3555 (p0) cc_final: 0.2899 (m-30) REVERT: I 230 TRP cc_start: 0.7852 (t-100) cc_final: 0.7339 (t60) REVERT: I 233 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7019 (pt) REVERT: I 317 TRP cc_start: 0.6740 (m-90) cc_final: 0.6317 (m-90) REVERT: I 323 LEU cc_start: 0.8692 (mp) cc_final: 0.8237 (tp) REVERT: I 328 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7333 (mpp) REVERT: I 363 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5281 (tp30) REVERT: J 42 LYS cc_start: 0.8643 (tptm) cc_final: 0.8396 (tptm) REVERT: J 46 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8181 (mm) REVERT: J 146 TRP cc_start: 0.8124 (m-10) cc_final: 0.7889 (m-10) REVERT: J 181 VAL cc_start: 0.6833 (m) cc_final: 0.6629 (p) REVERT: J 220 LEU cc_start: 0.7652 (mm) cc_final: 0.7351 (mm) REVERT: J 316 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5094 (pp) REVERT: J 330 MET cc_start: 0.7266 (mpm) cc_final: 0.6560 (ptt) REVERT: J 333 ILE cc_start: 0.7973 (pt) cc_final: 0.7587 (tp) outliers start: 109 outliers final: 77 residues processed: 293 average time/residue: 0.5510 time to fit residues: 195.8635 Evaluate side-chains 288 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 192 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 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 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 91 VAL Chi-restraints excluded: chain B residue 92 SER 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 B residue 301 LEU 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 148 CYS Chi-restraints excluded: chain C residue 289 VAL 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 64 SER 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 87 CYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 219 THR 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 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 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 559 ILE 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 42 VAL Chi-restraints excluded: chain H residue 57 THR 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 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 233 ILE Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 MET 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 251 HIS Chi-restraints excluded: chain J residue 316 LEU 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: 8.9990 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 246 optimal weight: 0.0970 chunk 302 optimal weight: 40.0000 chunk 164 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 23 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** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085405 restraints weight = 57238.889| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.39 r_work: 0.3120 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30752 Z= 0.107 Angle : 0.538 10.849 42201 Z= 0.279 Chirality : 0.040 0.162 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.477 91.901 5153 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 3.52 % Allowed : 32.83 % Favored : 63.66 % 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: 0.14 (0.15), residues: 3498 helix: 1.42 (0.16), residues: 1165 sheet: 0.61 (0.22), residues: 571 loop : -1.02 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.026 0.001 TYR J 44 PHE 0.028 0.001 PHE J 309 TRP 0.018 0.001 TRP J 381 HIS 0.007 0.000 HIS I 228 Details of bonding type rmsd covalent geometry : bond 0.00241 (30752) covalent geometry : angle 0.53777 (42201) hydrogen bonds : bond 0.03290 ( 1116) hydrogen bonds : angle 4.17312 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14383.56 seconds wall clock time: 244 minutes 26.41 seconds (14666.41 seconds total)