Starting phenix.real_space_refine on Sat Aug 8 21:34:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtp_65338/08_2026/9vtp_65338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtp_65338/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vtp_65338/08_2026/9vtp_65338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtp_65338/08_2026/9vtp_65338.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vtp_65338/08_2026/9vtp_65338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtp_65338/08_2026/9vtp_65338.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 97 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 18619 2.51 5 N 5150 2.21 5 O 5809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29818 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1221 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 7, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 24, 'rna3p': 32} Chain breaks: 1 Chain: "2" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 721 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "3" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2725 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2767 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2771 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain: "E" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2767 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain: "F" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2418 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2374 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 306} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2051 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2911 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 365} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 6, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 149 Chain: "J" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2670 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 340} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 8, 'PHE:plan': 5, 'ASN:plan1': 7, 'GLU:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 2, 'TRP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.21 Number of scatterers: 29818 At special positions: 0 Unit cell: (130.096, 193.264, 164.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 142 16.00 P 97 15.00 Mg 1 11.99 O 5809 8.00 N 5150 7.00 C 18619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 47 sheets defined 37.5% alpha, 16.3% beta 31 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.67 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: 6.13 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8091 1.33 - 1.45: 6575 1.45 - 1.58: 15706 1.58 - 1.70: 192 1.70 - 1.82: 188 Bond restraints: 30752 Sorted by residual: bond pdb=" C3' DG 2 27 " pdb=" C2' DG 2 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT 2 32 " pdb=" C2' DT 2 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DC 2 28 " pdb=" C2' DC 2 28 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG 2 37 " pdb=" C2' DG 2 37 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DA 2 26 " pdb=" C2' DA 2 26 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.42e+00 ... (remaining 30747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 41493 2.08 - 4.16: 629 4.16 - 6.24: 61 6.24 - 8.33: 11 8.33 - 10.41: 7 Bond angle restraints: 42201 Sorted by residual: angle pdb=" O4' C 1 34 " pdb=" C1' C 1 34 " pdb=" N1 C 1 34 " ideal model delta sigma weight residual 108.50 112.19 -3.69 7.00e-01 2.04e+00 2.78e+01 angle pdb=" O4' G 1 11 " pdb=" C1' G 1 11 " pdb=" N9 G 1 11 " ideal model delta sigma weight residual 108.50 112.17 -3.67 7.00e-01 2.04e+00 2.75e+01 angle pdb=" C ASN I 241 " pdb=" CA ASN I 241 " pdb=" CB ASN I 241 " ideal model delta sigma weight residual 115.79 110.18 5.61 1.19e+00 7.06e-01 2.22e+01 angle pdb=" N3 DT 2 55 " pdb=" C4 DT 2 55 " pdb=" O4 DT 2 55 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT 2 24 " pdb=" C4 DT 2 24 " pdb=" O4 DT 2 24 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (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: 3975 0.059 - 0.119: 579 0.119 - 0.178: 83 0.178 - 0.237: 1 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=" C2' C 1 34 " pdb=" C3' C 1 34 " pdb=" O2' C 1 34 " pdb=" C1' C 1 34 " both_signs ideal model delta sigma weight residual False -2.62 -2.81 0.19 2.00e-01 2.50e+01 8.88e-01 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 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 4636 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 6 " -0.033 2.00e-02 2.50e+03 1.56e-02 6.65e+00 pdb=" N9 A 1 6 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 1 6 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 6 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 6 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 1 6 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 6 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 11 " 0.033 2.00e-02 2.50e+03 1.45e-02 6.26e+00 pdb=" N9 G 1 11 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G 1 11 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 1 11 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 11 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 11 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 1 11 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G 1 11 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 1 11 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 1 11 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 1 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G 1 11 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 23 " 0.026 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" N1 U 1 23 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U 1 23 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U 1 23 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U 1 23 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U 1 23 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U 1 23 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U 1 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U 1 23 " -0.004 2.00e-02 2.50e+03 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5057 2.77 - 3.30: 28545 3.30 - 3.83: 51482 3.83 - 4.37: 61232 4.37 - 4.90: 102068 Nonbonded interactions: 248384 Sorted by model distance: nonbonded pdb=" OP2 A 1 6 " pdb="MG MG 1 101 " model vdw 2.236 2.170 nonbonded pdb=" N GLU G 268 " pdb=" OE1 GLU G 268 " model vdw 2.445 3.120 nonbonded pdb=" O5' DG 2 53 " pdb=" O4' DG 2 53 " model vdw 2.493 2.432 nonbonded pdb=" O GLU G 561 " pdb=" OE1 GLU G 561 " model vdw 2.502 3.040 nonbonded pdb=" O2' C 1 34 " pdb=" O4' U 1 35 " model vdw 2.505 3.040 ... (remaining 248379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'B' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'C' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'D' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = (chain 'E' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 through 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 345)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 13 through 84 or (resid 85 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 209 or (resid 210 throu \ gh 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thr \ ough 229 or (resid 230 through 242 and (name N or name CA or name C or name O or \ name CB )) or resid 243 through 251 or (resid 252 through 260 and (name N or na \ me CA or name C or name O or name CB )) or resid 261 or (resid 262 through 284 a \ nd (name N or name CA or name C or name O or name CB )) or resid 285 or (resid 2 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 287 through \ 319 or resid 330 through 356 or resid 373 through 395)) selection = (chain 'J' and ((resid 13 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 23 or (resid 24 and (name N or na \ me CA or name C or name O or name CB )) or resid 25 through 26 or (resid 27 and \ (name N or name CA or name C or name O or name CB )) or resid 28 through 31 or ( \ resid 32 through 63 and (name N or name CA or name C or name O or name CB )) or \ resid 64 through 189 or (resid 190 through 202 and (name N or name CA or name C \ or name O or name CB )) or resid 203 through 247 or (resid 248 and (name N or na \ me CA or name C or name O or name CB )) or resid 249 through 395)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.290 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: 0.670 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.590 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30752 Z= 0.183 Angle : 0.599 10.406 42201 Z= 0.373 Chirality : 0.044 0.296 4639 Planarity : 0.004 0.057 5094 Dihedral : 19.245 92.057 11511 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.79 % Allowed : 32.31 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3498 helix: 1.11 (0.16), residues: 1135 sheet: 0.40 (0.22), residues: 585 loop : -1.13 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.018 0.001 TYR I 171 PHE 0.025 0.001 PHE J 309 TRP 0.020 0.001 TRP J 381 HIS 0.004 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.18 (30752) covalent geometry : angle 0.59945 / 0.37 (42201) hydrogen bonds : bond 0.13207 / 14.39 ( 1116) hydrogen bonds : angle 5.43401 / 6.81 ( 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 : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8546 (mt0) cc_final: 0.8147 (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: 0.8169 (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: 0.8414 (m-10) REVERT: H 188 THR cc_start: 0.5048 (OUTLIER) cc_final: 0.4661 (t) REVERT: I 121 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6122 (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: 54 residues processed: 274 average time/residue: 0.5785 time to fit residues: 192.2062 Evaluate side-chains 248 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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... ** 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 = 0.3930 r_free = 0.3930 target = 0.128933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082069 restraints weight = 56642.764| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.34 r_work: 0.3043 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30752 Z= 0.191 Angle : 0.555 8.364 42201 Z= 0.297 Chirality : 0.042 0.235 4639 Planarity : 0.004 0.058 5094 Dihedral : 14.850 87.533 5218 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.17 % Allowed : 28.76 % Favored : 65.07 % 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: -0.18 (0.14), residues: 3498 helix: 1.12 (0.16), residues: 1158 sheet: 0.37 (0.22), residues: 592 loop : -1.17 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.015 0.001 TYR G 420 PHE 0.018 0.001 PHE E 302 TRP 0.013 0.001 TRP J 381 HIS 0.011 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (30752) covalent geometry : angle 0.55544 / 0.30 (42201) hydrogen bonds : bond 0.04713 / 4.90 ( 1116) hydrogen bonds : angle 4.71579 / 6.05 ( 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 371 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 192 time to evaluate : 1.102 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: 0.8961 (OUTLIER) cc_final: 0.8550 (tttm) REVERT: A 342 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8954 (pt) REVERT: B 47 LYS cc_start: 0.9300 (tppt) cc_final: 0.8896 (tppt) REVERT: B 55 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: B 118 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8994 (mm) REVERT: B 231 ASP cc_start: 0.7656 (p0) cc_final: 0.7437 (p0) REVERT: C 313 GLU cc_start: 0.8854 (pp20) cc_final: 0.8490 (pp20) REVERT: D 1 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7073 (ttm) REVERT: D 105 ASP cc_start: 0.8675 (t0) cc_final: 0.8125 (t0) REVERT: D 202 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: D 325 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: E 53 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8480 (p0) REVERT: E 86 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8735 (tp30) REVERT: F 215 PHE cc_start: 0.8739 (m-10) cc_final: 0.8522 (m-10) REVERT: F 344 GLN cc_start: 0.8073 (tt0) cc_final: 0.7862 (tt0) REVERT: G 105 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8101 (m90) REVERT: G 260 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8766 (mtt) REVERT: H 29 HIS cc_start: 0.5540 (t70) cc_final: 0.5164 (t70) REVERT: H 31 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: H 188 THR cc_start: 0.5188 (OUTLIER) cc_final: 0.4982 (t) REVERT: I 138 GLU cc_start: 0.5949 (tm-30) cc_final: 0.5087 (mt-10) REVERT: I 163 GLU cc_start: 0.4730 (OUTLIER) cc_final: 0.4508 (tp30) REVERT: I 172 ASP cc_start: 0.3720 (p0) cc_final: 0.2841 (m-30) REVERT: I 283 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (tp) REVERT: I 317 TRP cc_start: 0.6729 (m-90) cc_final: 0.6383 (m-90) REVERT: J 28 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5694 (tttt) REVERT: J 69 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8260 (mmpt) REVERT: J 146 TRP cc_start: 0.8089 (m-10) cc_final: 0.7796 (m-10) REVERT: J 222 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4882 (m-80) REVERT: J 330 MET cc_start: 0.6908 (mpm) cc_final: 0.6294 (ptt) outliers start: 179 outliers final: 76 residues processed: 348 average time/residue: 0.5395 time to fit residues: 229.5552 Evaluate side-chains 278 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 184 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 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 91 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 118 LEU 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 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE 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 J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 218 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082029 restraints weight = 57371.682| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.40 r_work: 0.3065 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30752 Z= 0.132 Angle : 0.523 8.177 42201 Z= 0.280 Chirality : 0.041 0.285 4639 Planarity : 0.004 0.060 5094 Dihedral : 14.696 87.868 5174 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.86 % Allowed : 29.34 % Favored : 64.79 % 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: 0.39 (0.22), residues: 592 loop : -1.15 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 110 TYR 0.017 0.001 TYR E 52 PHE 0.015 0.001 PHE E 302 TRP 0.012 0.001 TRP J 381 HIS 0.012 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (30752) covalent geometry : angle 0.52314 / 0.28 (42201) hydrogen bonds : bond 0.04069 / 4.21 ( 1116) hydrogen bonds : angle 4.53937 / 5.81 ( 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 370 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 200 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: A 342 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8945 (pt) REVERT: B 47 LYS cc_start: 0.9276 (tppt) cc_final: 0.8863 (tppt) REVERT: B 55 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7821 (pp30) REVERT: C 86 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8533 (tp30) REVERT: C 313 GLU cc_start: 0.8844 (pp20) cc_final: 0.8469 (pp20) REVERT: D 105 ASP cc_start: 0.8614 (t0) cc_final: 0.8062 (t0) REVERT: D 163 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6640 (p0) REVERT: D 202 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: D 325 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8244 (ttp) REVERT: E 53 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8449 (p0) REVERT: E 86 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8686 (tp30) REVERT: F 215 PHE cc_start: 0.8726 (m-10) cc_final: 0.8395 (m-10) REVERT: G 105 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (m90) REVERT: G 260 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8735 (mtt) REVERT: G 510 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7948 (mtp180) REVERT: H 29 HIS cc_start: 0.5658 (t70) cc_final: 0.5285 (t-170) REVERT: H 31 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: H 188 THR cc_start: 0.5230 (OUTLIER) cc_final: 0.5012 (t) REVERT: I 138 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5039 (mt-10) REVERT: I 163 GLU cc_start: 0.4736 (OUTLIER) cc_final: 0.4505 (tp30) REVERT: I 172 ASP cc_start: 0.3782 (p0) cc_final: 0.2896 (m-30) REVERT: I 230 TRP cc_start: 0.7599 (t-100) cc_final: 0.7157 (t60) REVERT: I 233 ILE cc_start: 0.7526 (pp) cc_final: 0.6953 (pt) REVERT: I 317 TRP cc_start: 0.6699 (m-90) cc_final: 0.6330 (m-90) REVERT: I 363 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5346 (mm-30) REVERT: J 28 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5679 (tttt) REVERT: J 69 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8268 (mmpt) REVERT: J 146 TRP cc_start: 0.8061 (m-10) cc_final: 0.7793 (m-10) REVERT: J 222 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.4889 (m-80) REVERT: J 330 MET cc_start: 0.6933 (mpm) cc_final: 0.6271 (ptt) REVERT: J 353 LEU cc_start: 0.2427 (OUTLIER) cc_final: 0.1595 (mm) outliers start: 170 outliers final: 85 residues processed: 344 average time/residue: 0.5564 time to fit residues: 232.2298 Evaluate side-chains 296 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 191 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 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 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 86 GLU 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 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 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 116 ILE 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 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 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 516 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 373 TYR 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: 3.9990 chunk 138 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 221 optimal weight: 0.1980 chunk 326 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 296 ASN H 90 GLN I 267 ASN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 310 GLN J 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083508 restraints weight = 56990.409| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.38 r_work: 0.3086 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30752 Z= 0.112 Angle : 0.510 8.129 42201 Z= 0.272 Chirality : 0.040 0.268 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.663 88.097 5166 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 5.76 % Allowed : 29.83 % Favored : 64.41 % 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: 1166 sheet: 0.48 (0.22), residues: 570 loop : -1.11 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 110 TYR 0.015 0.001 TYR H 138 PHE 0.014 0.001 PHE E 302 TRP 0.010 0.001 TRP J 381 HIS 0.011 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (30752) covalent geometry : angle 0.50992 / 0.27 (42201) hydrogen bonds : bond 0.03751 / 3.87 ( 1116) hydrogen bonds : angle 4.42496 / 5.67 ( 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 367 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 200 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8761 (mt0) cc_final: 0.8461 (mt0) REVERT: A 324 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: A 342 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8949 (pt) REVERT: B 47 LYS cc_start: 0.9248 (tppt) cc_final: 0.8843 (tppt) REVERT: B 55 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: B 231 ASP cc_start: 0.7691 (p0) cc_final: 0.7442 (p0) REVERT: C 313 GLU cc_start: 0.8839 (pp20) cc_final: 0.8469 (pp20) REVERT: D 105 ASP cc_start: 0.8555 (t0) cc_final: 0.7978 (t0) REVERT: D 163 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6706 (p0) REVERT: D 325 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: E 53 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8441 (p0) REVERT: E 86 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8650 (tp30) REVERT: F 215 PHE cc_start: 0.8714 (m-10) cc_final: 0.8484 (m-10) REVERT: G 105 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.8039 (m90) REVERT: G 260 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8730 (mtt) REVERT: G 510 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7909 (mtp180) REVERT: H 15 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5448 (ptt90) REVERT: H 29 HIS cc_start: 0.5626 (t70) cc_final: 0.4971 (t-170) REVERT: H 33 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: H 54 ARG cc_start: 0.3935 (OUTLIER) cc_final: 0.2962 (mtt-85) REVERT: H 188 THR cc_start: 0.5230 (OUTLIER) cc_final: 0.5009 (t) REVERT: I 163 GLU cc_start: 0.4724 (OUTLIER) cc_final: 0.4503 (tp30) REVERT: I 172 ASP cc_start: 0.3743 (p0) cc_final: 0.2860 (m-30) REVERT: I 230 TRP cc_start: 0.7642 (t-100) cc_final: 0.7182 (t60) REVERT: I 233 ILE cc_start: 0.7520 (pp) cc_final: 0.6960 (pt) REVERT: I 317 TRP cc_start: 0.6706 (m-90) cc_final: 0.6353 (m-90) REVERT: I 363 GLU cc_start: 0.5877 (OUTLIER) cc_final: 0.5340 (tp30) REVERT: J 28 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5637 (tttt) REVERT: J 69 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8259 (mmpt) REVERT: J 146 TRP cc_start: 0.8061 (m-10) cc_final: 0.7819 (m-10) REVERT: J 222 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.4923 (m-80) REVERT: J 330 MET cc_start: 0.6956 (mpm) cc_final: 0.6290 (ptt) outliers start: 167 outliers final: 77 residues processed: 347 average time/residue: 0.5274 time to fit residues: 221.8766 Evaluate side-chains 280 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 185 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 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 164 GLU Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 239 THR 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 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 15 ARG Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 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 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 334 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 242 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 343 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 271 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.130577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083465 restraints weight = 57296.849| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.38 r_work: 0.3083 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0804 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= 0.121 Angle : 0.513 8.222 42201 Z= 0.273 Chirality : 0.040 0.208 4639 Planarity : 0.004 0.059 5094 Dihedral : 14.584 88.413 5161 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 6.03 % Allowed : 29.59 % 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: -0.03 (0.14), residues: 3498 helix: 1.28 (0.16), residues: 1164 sheet: 0.50 (0.22), residues: 572 loop : -1.10 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 110 TYR 0.016 0.001 TYR H 138 PHE 0.014 0.001 PHE E 302 TRP 0.010 0.001 TRP J 36 HIS 0.010 0.000 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (30752) covalent geometry : angle 0.51326 / 0.27 (42201) hydrogen bonds : bond 0.03705 / 3.83 ( 1116) hydrogen bonds : angle 4.38997 / 5.64 ( 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: 175 poor density : 199 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8766 (mt0) cc_final: 0.8455 (mt0) REVERT: A 230 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8726 (tptp) REVERT: A 342 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8935 (pt) REVERT: B 47 LYS cc_start: 0.9248 (tppt) cc_final: 0.8840 (tppt) REVERT: B 55 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7825 (pp30) REVERT: C 313 GLU cc_start: 0.8835 (pp20) cc_final: 0.8453 (pp20) REVERT: D 163 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.6647 (p0) REVERT: D 202 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: D 325 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (ttp) REVERT: E 53 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (p0) REVERT: E 86 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8677 (tp30) REVERT: E 154 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9013 (mm) REVERT: E 184 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8667 (mmm-85) REVERT: F 215 PHE cc_start: 0.8712 (m-10) cc_final: 0.8469 (m-10) REVERT: F 286 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7837 (ttt90) REVERT: G 105 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.8029 (m90) REVERT: G 260 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8735 (mtt) REVERT: G 510 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7911 (mtp180) REVERT: H 29 HIS cc_start: 0.5661 (t70) cc_final: 0.4949 (t-170) REVERT: H 33 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5726 (m-10) REVERT: H 188 THR cc_start: 0.5330 (OUTLIER) cc_final: 0.5099 (t) REVERT: I 163 GLU cc_start: 0.4767 (OUTLIER) cc_final: 0.4535 (tp30) REVERT: I 172 ASP cc_start: 0.3703 (OUTLIER) cc_final: 0.2790 (m-30) REVERT: I 230 TRP cc_start: 0.7664 (t-100) cc_final: 0.7175 (t60) REVERT: I 233 ILE cc_start: 0.7551 (pp) cc_final: 0.7035 (pt) REVERT: I 317 TRP cc_start: 0.6729 (m-90) cc_final: 0.6319 (m-90) REVERT: I 352 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7974 (mm) REVERT: I 363 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5326 (tp30) REVERT: J 28 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5664 (tttt) REVERT: J 69 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8232 (mmpt) REVERT: J 146 TRP cc_start: 0.8065 (m-10) cc_final: 0.7832 (m-10) REVERT: J 222 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: J 316 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.4909 (pp) REVERT: J 330 MET cc_start: 0.7005 (mpm) cc_final: 0.6333 (ptt) outliers start: 175 outliers final: 96 residues processed: 349 average time/residue: 0.5535 time to fit residues: 234.7362 Evaluate side-chains 305 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 186 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 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 318 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 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 247 ASP Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 194 LYS 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 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 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 572 CYS 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 25 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 121 ARG 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 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: 5.9990 chunk 222 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 349 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 229 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN G 147 HIS H 32 ASN H 90 GLN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079313 restraints weight = 56639.508| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.34 r_work: 0.2998 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30752 Z= 0.312 Angle : 0.653 9.006 42201 Z= 0.343 Chirality : 0.046 0.326 4639 Planarity : 0.005 0.061 5094 Dihedral : 14.641 87.101 5160 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 7.31 % Allowed : 28.45 % Favored : 64.24 % 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: -0.37 (0.14), residues: 3498 helix: 0.90 (0.15), residues: 1170 sheet: 0.35 (0.22), residues: 582 loop : -1.28 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 110 TYR 0.019 0.002 TYR H 138 PHE 0.024 0.002 PHE C 302 TRP 0.020 0.002 TRP J 381 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (30752) covalent geometry : angle 0.65271 / 0.34 (42201) hydrogen bonds : bond 0.05071 / 5.21 ( 1116) hydrogen bonds : angle 4.69472 / 6.07 ( 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 404 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 192 time to evaluate : 1.134 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: 0.9048 (OUTLIER) cc_final: 0.8663 (tttm) REVERT: A 324 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 342 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8989 (pt) REVERT: B 47 LYS cc_start: 0.9314 (tppt) cc_final: 0.8920 (tppt) REVERT: B 118 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9023 (mm) REVERT: B 167 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8529 (pp) REVERT: C 313 GLU cc_start: 0.8848 (pp20) cc_final: 0.8509 (pp20) REVERT: D 105 ASP cc_start: 0.8682 (t0) cc_final: 0.8219 (t0) REVERT: D 202 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: D 315 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9160 (mp) REVERT: E 53 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8446 (p0) REVERT: F 28 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7621 (ttp-110) REVERT: F 29 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9174 (mtmt) REVERT: F 215 PHE cc_start: 0.8786 (m-10) cc_final: 0.8527 (m-10) REVERT: G 105 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.8083 (m90) REVERT: G 260 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8787 (mtt) REVERT: G 510 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8023 (mtp180) REVERT: G 585 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7710 (tmm160) REVERT: H 15 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5148 (ptt90) REVERT: H 29 HIS cc_start: 0.5787 (t70) cc_final: 0.5373 (t-170) REVERT: H 33 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.5713 (m-10) REVERT: H 54 ARG cc_start: 0.3842 (OUTLIER) cc_final: 0.2859 (mtt-85) REVERT: H 90 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6202 (tm130) REVERT: H 188 THR cc_start: 0.5266 (OUTLIER) cc_final: 0.5046 (t) REVERT: I 72 SER cc_start: 0.2077 (OUTLIER) cc_final: 0.1839 (p) REVERT: I 163 GLU cc_start: 0.4757 (OUTLIER) cc_final: 0.4541 (tp30) REVERT: I 172 ASP cc_start: 0.3823 (OUTLIER) cc_final: 0.2968 (m-30) REVERT: I 230 TRP cc_start: 0.7730 (t-100) cc_final: 0.7235 (t60) REVERT: I 233 ILE cc_start: 0.7689 (pp) cc_final: 0.7334 (pt) REVERT: I 317 TRP cc_start: 0.6803 (m-90) cc_final: 0.6416 (m-90) REVERT: I 363 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5279 (tp30) REVERT: J 28 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5646 (tttt) REVERT: J 222 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: J 224 TRP cc_start: 0.6574 (OUTLIER) cc_final: 0.5608 (t-100) REVERT: J 302 ASN cc_start: 0.4474 (OUTLIER) cc_final: 0.3466 (p0) REVERT: J 330 MET cc_start: 0.7122 (mpm) cc_final: 0.6408 (ptt) outliers start: 212 outliers final: 108 residues processed: 376 average time/residue: 0.5403 time to fit residues: 247.6180 Evaluate side-chains 319 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 184 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 180 THR 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 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 60 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 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 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 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 572 CYS Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 585 ARG Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 31 PHE 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 90 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 316 LEU 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 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 90 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 347 optimal weight: 30.0000 chunk 213 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 0.0050 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN D 296 ASN H 90 GLN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 ASN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081538 restraints weight = 56878.987| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.40 r_work: 0.3042 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30752 Z= 0.139 Angle : 0.556 8.454 42201 Z= 0.296 Chirality : 0.042 0.263 4639 Planarity : 0.004 0.060 5094 Dihedral : 14.622 87.596 5160 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 5.45 % Allowed : 30.48 % 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: -0.23 (0.14), residues: 3498 helix: 1.07 (0.16), residues: 1166 sheet: 0.38 (0.22), residues: 580 loop : -1.21 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 110 TYR 0.022 0.001 TYR J 44 PHE 0.016 0.001 PHE E 302 TRP 0.017 0.001 TRP J 381 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (30752) covalent geometry : angle 0.55555 / 0.30 (42201) hydrogen bonds : bond 0.04027 / 4.16 ( 1116) hydrogen bonds : angle 4.51964 / 5.82 ( 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 345 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 187 time to evaluate : 0.974 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: 0.8810 (mt0) cc_final: 0.8520 (mt0) REVERT: A 321 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8219 (mm) REVERT: A 342 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8967 (pt) REVERT: B 47 LYS cc_start: 0.9263 (tppt) cc_final: 0.8865 (tppt) REVERT: B 231 ASP cc_start: 0.7662 (p0) cc_final: 0.7385 (p0) REVERT: C 313 GLU cc_start: 0.8847 (pp20) cc_final: 0.8470 (pp20) REVERT: D 202 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: E 53 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8398 (p0) REVERT: E 154 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9012 (mm) REVERT: F 215 PHE cc_start: 0.8741 (m-10) cc_final: 0.8504 (m-10) REVERT: G 105 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.8082 (m90) REVERT: G 260 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8754 (mtt) REVERT: G 510 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7972 (mtp180) REVERT: G 585 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7734 (tmm160) REVERT: H 15 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5120 (ptt90) REVERT: H 29 HIS cc_start: 0.5632 (t70) cc_final: 0.5091 (t-170) REVERT: H 31 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: H 33 TYR cc_start: 0.5839 (m-10) cc_final: 0.5631 (m-10) REVERT: H 54 ARG cc_start: 0.3943 (OUTLIER) cc_final: 0.2889 (mtt-85) REVERT: H 188 THR cc_start: 0.5416 (OUTLIER) cc_final: 0.5192 (t) REVERT: I 71 HIS cc_start: 0.6002 (m-70) cc_final: 0.5780 (m90) REVERT: I 163 GLU cc_start: 0.4789 (OUTLIER) cc_final: 0.4567 (tp30) REVERT: I 172 ASP cc_start: 0.3804 (OUTLIER) cc_final: 0.2948 (m-30) REVERT: I 230 TRP cc_start: 0.7700 (t-100) cc_final: 0.7194 (t60) REVERT: I 233 ILE cc_start: 0.7678 (pp) cc_final: 0.7286 (pt) REVERT: I 317 TRP cc_start: 0.6707 (m-90) cc_final: 0.6330 (m-90) REVERT: I 328 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7268 (mpp) REVERT: I 363 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5226 (tp30) REVERT: J 28 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5617 (tttt) REVERT: J 222 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4990 (m-80) REVERT: J 224 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.5564 (t-100) REVERT: J 316 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4888 (pp) REVERT: J 330 MET cc_start: 0.6973 (mpm) cc_final: 0.6149 (ptt) outliers start: 158 outliers final: 91 residues processed: 325 average time/residue: 0.5506 time to fit residues: 215.4418 Evaluate side-chains 291 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 179 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain 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 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 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 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 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 15 ARG Chi-restraints excluded: chain H residue 31 PHE 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 142 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 281 LYS 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 28 LYS Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 350 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 126 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 305 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.129488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082899 restraints weight = 56533.515| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.35 r_work: 0.3057 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30752 Z= 0.142 Angle : 0.550 9.413 42201 Z= 0.291 Chirality : 0.041 0.242 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.599 87.532 5160 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 5.38 % Allowed : 30.59 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3498 helix: 1.14 (0.16), residues: 1168 sheet: 0.38 (0.22), residues: 570 loop : -1.17 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 110 TYR 0.014 0.001 TYR A 80 PHE 0.016 0.001 PHE E 302 TRP 0.016 0.001 TRP J 146 HIS 0.010 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (30752) covalent geometry : angle 0.54966 / 0.29 (42201) hydrogen bonds : bond 0.03894 / 4.03 ( 1116) hydrogen bonds : angle 4.45609 / 5.75 ( 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 345 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 189 time to evaluate : 0.998 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: 0.8784 (mt0) cc_final: 0.8481 (mt0) REVERT: A 321 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8196 (mm) REVERT: A 324 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 342 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8972 (pt) REVERT: B 47 LYS cc_start: 0.9239 (tppt) cc_final: 0.8750 (tppt) REVERT: B 55 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7834 (pp30) REVERT: C 313 GLU cc_start: 0.8834 (pp20) cc_final: 0.8453 (pp20) REVERT: D 163 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.6528 (p0) REVERT: D 202 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: E 53 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8405 (p0) REVERT: E 86 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: E 154 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.8997 (mm) REVERT: F 215 PHE cc_start: 0.8748 (m-10) cc_final: 0.8518 (m-10) REVERT: G 105 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8064 (m90) REVERT: G 260 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8754 (mtt) REVERT: G 510 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7949 (mtp180) REVERT: H 29 HIS cc_start: 0.5816 (t70) cc_final: 0.5256 (t-170) REVERT: H 163 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7502 (ptp-110) REVERT: H 188 THR cc_start: 0.5410 (OUTLIER) cc_final: 0.5177 (t) REVERT: I 71 HIS cc_start: 0.6004 (m-70) cc_final: 0.5786 (m90) REVERT: I 163 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4581 (tp30) REVERT: I 172 ASP cc_start: 0.3830 (OUTLIER) cc_final: 0.2968 (m-30) REVERT: I 230 TRP cc_start: 0.7750 (t-100) cc_final: 0.7231 (t60) REVERT: I 233 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7246 (pt) REVERT: I 283 ILE cc_start: 0.8436 (mm) cc_final: 0.8203 (mp) REVERT: I 317 TRP cc_start: 0.6732 (m-90) cc_final: 0.6306 (m-90) REVERT: I 323 LEU cc_start: 0.8725 (mp) cc_final: 0.8267 (tp) REVERT: I 328 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7182 (mpp) REVERT: I 352 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8007 (mm) REVERT: I 363 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5247 (tp30) REVERT: J 46 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8400 (mm) REVERT: J 117 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5534 (tm-30) REVERT: J 222 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.5301 (m-80) REVERT: J 224 TRP cc_start: 0.6615 (OUTLIER) cc_final: 0.5761 (t-100) REVERT: J 302 ASN cc_start: 0.4437 (OUTLIER) cc_final: 0.3115 (p0) REVERT: J 316 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4948 (pp) REVERT: J 330 MET cc_start: 0.6810 (mpm) cc_final: 0.5997 (ptt) outliers start: 156 outliers final: 98 residues processed: 325 average time/residue: 0.5179 time to fit residues: 203.8620 Evaluate side-chains 304 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 180 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 99 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 318 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 154 ILE 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 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 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 H residue 20 ILE 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 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 155 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 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 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 350 GLN 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: 6.9990 chunk 352 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081697 restraints weight = 56619.410| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.31 r_work: 0.3028 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30752 Z= 0.220 Angle : 0.593 10.034 42201 Z= 0.312 Chirality : 0.043 0.243 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.588 87.245 5160 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 5.24 % Allowed : 30.93 % 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: -0.28 (0.14), residues: 3498 helix: 1.02 (0.16), residues: 1172 sheet: 0.31 (0.22), residues: 578 loop : -1.21 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 110 TYR 0.017 0.001 TYR E 52 PHE 0.020 0.002 PHE C 302 TRP 0.016 0.001 TRP J 146 HIS 0.009 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (30752) covalent geometry : angle 0.59258 / 0.31 (42201) hydrogen bonds : bond 0.04261 / 4.41 ( 1116) hydrogen bonds : angle 4.54298 / 5.88 ( 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: 152 poor density : 182 time to evaluate : 1.023 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 321 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8272 (mm) REVERT: A 324 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: A 342 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8971 (pt) REVERT: B 47 LYS cc_start: 0.9239 (tppt) cc_final: 0.8740 (tppt) REVERT: B 118 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8962 (mm) REVERT: C 313 GLU cc_start: 0.8846 (pp20) cc_final: 0.8459 (pp20) REVERT: D 202 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: E 53 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8439 (p0) REVERT: E 154 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9019 (mm) REVERT: F 215 PHE cc_start: 0.8782 (m-10) cc_final: 0.8539 (m-10) REVERT: G 105 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.8085 (m90) REVERT: G 260 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: G 510 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7997 (mtp180) REVERT: G 585 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7741 (tmm160) REVERT: H 188 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.5089 (t) REVERT: I 71 HIS cc_start: 0.5936 (m-70) cc_final: 0.5697 (m90) REVERT: I 172 ASP cc_start: 0.3928 (OUTLIER) cc_final: 0.3027 (m-30) REVERT: I 230 TRP cc_start: 0.7773 (t-100) cc_final: 0.7246 (t60) REVERT: I 233 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7285 (pt) REVERT: I 283 ILE cc_start: 0.8434 (mm) cc_final: 0.8199 (mp) REVERT: I 308 MET cc_start: 0.7658 (ttm) cc_final: 0.7404 (ptp) REVERT: I 317 TRP cc_start: 0.6771 (m-90) cc_final: 0.6290 (m-90) REVERT: I 323 LEU cc_start: 0.8726 (mp) cc_final: 0.8284 (tp) REVERT: I 328 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: I 352 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8061 (mm) REVERT: I 363 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5150 (tp30) REVERT: J 46 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8423 (mm) REVERT: J 222 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: J 224 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.5758 (t-100) REVERT: J 316 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.4986 (pp) REVERT: J 330 MET cc_start: 0.6874 (mpm) cc_final: 0.6017 (ptp) outliers start: 152 outliers final: 101 residues processed: 319 average time/residue: 0.5280 time to fit residues: 205.8503 Evaluate side-chains 296 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 174 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 154 ILE 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 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 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 286 ARG Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 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 585 ARG Chi-restraints excluded: chain H residue 20 ILE 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 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 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 352 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 350 GLN 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: 0.4980 chunk 116 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 253 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 258 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** I 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083731 restraints weight = 56735.760| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.40 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30752 Z= 0.115 Angle : 0.548 10.157 42201 Z= 0.290 Chirality : 0.041 0.222 4639 Planarity : 0.004 0.061 5094 Dihedral : 14.578 87.882 5160 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 3.83 % Allowed : 32.38 % Favored : 63.79 % 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: -0.12 (0.14), residues: 3498 helix: 1.20 (0.16), residues: 1162 sheet: 0.40 (0.22), residues: 572 loop : -1.13 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.013 0.001 TYR D 150 PHE 0.012 0.001 PHE E 302 TRP 0.017 0.001 TRP J 146 HIS 0.006 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (30752) covalent geometry : angle 0.54778 / 0.29 (42201) hydrogen bonds : bond 0.03644 / 3.78 ( 1116) hydrogen bonds : angle 4.39975 / 5.66 ( 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 300 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 189 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8788 (mt0) cc_final: 0.8491 (mt0) REVERT: A 118 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9152 (mm) REVERT: A 324 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 342 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8965 (pt) REVERT: B 47 LYS cc_start: 0.9203 (tppt) cc_final: 0.8716 (tppt) REVERT: B 118 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8928 (mm) REVERT: C 313 GLU cc_start: 0.8826 (pp20) cc_final: 0.8473 (pp20) REVERT: D 163 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6635 (p0) REVERT: D 202 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: E 53 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8405 (p0) REVERT: E 86 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8680 (tp30) REVERT: F 215 PHE cc_start: 0.8725 (m-10) cc_final: 0.8524 (m-10) REVERT: G 105 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.8041 (m90) REVERT: G 260 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8744 (mtt) REVERT: G 510 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: H 29 HIS cc_start: 0.5886 (t70) cc_final: 0.5484 (t70) REVERT: H 163 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7546 (ptm160) REVERT: H 188 THR cc_start: 0.5394 (OUTLIER) cc_final: 0.5154 (t) REVERT: I 71 HIS cc_start: 0.5976 (m-70) cc_final: 0.5753 (m90) REVERT: I 172 ASP cc_start: 0.3652 (p0) cc_final: 0.2964 (m-30) REVERT: I 230 TRP cc_start: 0.7761 (t-100) cc_final: 0.7236 (t60) REVERT: I 233 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7178 (pt) REVERT: I 283 ILE cc_start: 0.8425 (mm) cc_final: 0.8205 (mp) REVERT: I 308 MET cc_start: 0.7643 (ttm) cc_final: 0.7403 (ptp) REVERT: I 317 TRP cc_start: 0.6724 (m-90) cc_final: 0.6258 (m-90) REVERT: I 323 LEU cc_start: 0.8751 (mp) cc_final: 0.8265 (tp) REVERT: I 328 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7207 (mpp) REVERT: I 363 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5338 (tp30) REVERT: I 384 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8016 (mm-30) REVERT: J 46 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8453 (mm) REVERT: J 54 GLN cc_start: 0.8200 (pm20) cc_final: 0.7850 (pm20) REVERT: J 222 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: J 224 TRP cc_start: 0.6651 (OUTLIER) cc_final: 0.5676 (t-100) REVERT: J 302 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.2913 (p0) REVERT: J 316 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.4956 (pp) REVERT: J 330 MET cc_start: 0.6820 (mpm) cc_final: 0.5983 (ptp) outliers start: 111 outliers final: 71 residues processed: 287 average time/residue: 0.5669 time to fit residues: 197.8380 Evaluate side-chains 276 residues out of total 3134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 184 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 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 C residue 3 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 231 ASP 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 309 ASP Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 489 CYS Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 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 54 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 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 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 368 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 224 TRP Chi-restraints excluded: chain J residue 251 HIS Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 334 CYS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 350 GLN 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: 0.4980 chunk 101 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 177 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN D 67 GLN ** 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 302 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083996 restraints weight = 57209.414| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.39 r_work: 0.3089 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 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 : 0.002 0.049 30752 Z= 0.112 Angle : 0.542 10.312 42201 Z= 0.286 Chirality : 0.041 0.198 4639 Planarity : 0.004 0.063 5094 Dihedral : 14.544 88.087 5158 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.43 % Rotamer: Outliers : 3.79 % Allowed : 32.45 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3498 helix: 1.28 (0.16), residues: 1156 sheet: 0.44 (0.22), residues: 572 loop : -1.11 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 110 TYR 0.027 0.001 TYR J 44 PHE 0.020 0.001 PHE J 22 TRP 0.016 0.001 TRP J 146 HIS 0.012 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (30752) covalent geometry : angle 0.54236 / 0.29 (42201) hydrogen bonds : bond 0.03627 / 3.76 ( 1116) hydrogen bonds : angle 4.35172 / 5.60 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13857.91 seconds wall clock time: 235 minutes 44.18 seconds (14144.18 seconds total)