Starting phenix.real_space_refine on Thu Mar 5 09:30:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.map" model { file = "/net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0b_13743/03_2026/7q0b_13743.cif" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 104 5.16 5 C 13542 2.51 5 N 3634 2.21 5 O 3886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5026 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 2 Chain: "C" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5026 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 2 Chain: "D" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "E" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "G" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Time building chain proxies: 5.01, per 1000 atoms: 0.24 Number of scatterers: 21168 At special positions: 0 Unit cell: (124.89, 111.858, 137.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 2 15.00 O 3886 8.00 N 3634 7.00 C 13542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 945.9 milliseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 12 sheets defined 54.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.595A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.727A pdb=" N SER A 122 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.749A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 168 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.940A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.202A pdb=" N ARG A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.224A pdb=" N PHE A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.505A pdb=" N PHE A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 410 removed outlier: 3.678A pdb=" N LEU A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.556A pdb=" N THR A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 592 through 596 removed outlier: 3.545A pdb=" N LEU A 595 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.596A pdb=" N VAL B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.732A pdb=" N SER B 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 123 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 124' Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.764A pdb=" N GLY B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 168 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.970A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.201A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.235A pdb=" N PHE B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 410 removed outlier: 3.688A pdb=" N LEU B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 498 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 591 removed outlier: 3.513A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.574A pdb=" N LEU B 595 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.596A pdb=" N VAL C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.730A pdb=" N SER C 122 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA C 123 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TRP C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 124' Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.742A pdb=" N GLY C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 168 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 184 through 194 removed outlier: 3.962A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.200A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 288 removed outlier: 4.230A pdb=" N PHE C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.526A pdb=" N PHE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 410 removed outlier: 3.680A pdb=" N LEU C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 498 Processing helix chain 'C' and resid 513 through 522 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 578 through 591 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.552A pdb=" N LEU C 595 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.596A pdb=" N VAL D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.729A pdb=" N SER D 122 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA D 123 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.747A pdb=" N GLY D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 168 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.964A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 4.200A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 288 removed outlier: 4.233A pdb=" N PHE D 287 " --> pdb=" O ASN D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 312 Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.526A pdb=" N PHE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 410 removed outlier: 3.688A pdb=" N LEU D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 498 Processing helix chain 'D' and resid 513 through 522 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 591 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.536A pdb=" N LEU D 595 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 337 through 346 removed outlier: 3.917A pdb=" N ILE E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.929A pdb=" N ILE F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 337 through 346 removed outlier: 3.930A pdb=" N ILE G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 328 Processing helix chain 'H' and resid 337 through 346 removed outlier: 3.933A pdb=" N ILE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.820A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 65 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 28 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS A 178 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 257 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.179A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 526 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.974A pdb=" N ASN A 374 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.828A pdb=" N TYR B 62 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 115 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 65 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 28 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N HIS B 178 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 257 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.185A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 328 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 526 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.980A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.825A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 65 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 28 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS C 178 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 257 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.185A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 526 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.994A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.826A pdb=" N TYR D 62 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL D 115 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 64 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 117 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 66 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 65 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL D 28 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N HIS D 178 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 257 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 477 removed outlier: 6.183A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER D 526 " --> pdb=" O TYR D 551 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.978A pdb=" N ASN D 374 " --> pdb=" O ASN D 447 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6906 1.34 - 1.46: 3823 1.46 - 1.57: 10827 1.57 - 1.69: 8 1.69 - 1.80: 156 Bond restraints: 21720 Sorted by residual: bond pdb=" CA ASP D 135 " pdb=" C ASP D 135 " ideal model delta sigma weight residual 1.523 1.505 0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" C ARG B 638 " pdb=" N PRO B 639 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" CA VAL C 642 " pdb=" C VAL C 642 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.12e-01 bond pdb=" CA PRO D 639 " pdb=" C PRO D 639 " ideal model delta sigma weight residual 1.527 1.516 0.011 1.35e-02 5.49e+03 6.68e-01 bond pdb=" CB PRO D 639 " pdb=" CG PRO D 639 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.24e-01 ... (remaining 21715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 28680 1.45 - 2.90: 602 2.90 - 4.35: 114 4.35 - 5.80: 17 5.80 - 7.25: 13 Bond angle restraints: 29426 Sorted by residual: angle pdb=" N ARG B 638 " pdb=" CA ARG B 638 " pdb=" C ARG B 638 " ideal model delta sigma weight residual 109.81 116.74 -6.93 2.21e+00 2.05e-01 9.85e+00 angle pdb=" C SER A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 121.70 125.93 -4.23 1.80e+00 3.09e-01 5.52e+00 angle pdb=" C ARG D 638 " pdb=" N PRO D 639 " pdb=" CA PRO D 639 " ideal model delta sigma weight residual 121.65 119.44 2.21 1.01e+00 9.80e-01 4.77e+00 angle pdb=" CA LEU B 488 " pdb=" CB LEU B 488 " pdb=" CG LEU B 488 " ideal model delta sigma weight residual 116.30 123.55 -7.25 3.50e+00 8.16e-02 4.29e+00 angle pdb=" CA LEU A 488 " pdb=" CB LEU A 488 " pdb=" CG LEU A 488 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 ... (remaining 29421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11412 17.85 - 35.71: 1090 35.71 - 53.56: 203 53.56 - 71.41: 47 71.41 - 89.26: 40 Dihedral angle restraints: 12792 sinusoidal: 5174 harmonic: 7618 Sorted by residual: dihedral pdb=" CA ARG B 638 " pdb=" C ARG B 638 " pdb=" N PRO B 639 " pdb=" CA PRO B 639 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU C 488 " pdb=" C LEU C 488 " pdb=" N LEU C 489 " pdb=" CA LEU C 489 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU D 488 " pdb=" C LEU D 488 " pdb=" N LEU D 489 " pdb=" CA LEU D 489 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1957 0.033 - 0.065: 833 0.065 - 0.098: 219 0.098 - 0.130: 97 0.130 - 0.163: 20 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CA THR C 515 " pdb=" N THR C 515 " pdb=" C THR C 515 " pdb=" CB THR C 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA THR D 515 " pdb=" N THR D 515 " pdb=" C THR D 515 " pdb=" CB THR D 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA THR A 515 " pdb=" N THR A 515 " pdb=" C THR A 515 " pdb=" CB THR A 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 3123 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 638 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 639 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 639 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 639 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 303 " -0.127 9.50e-02 1.11e+02 5.70e-02 2.33e+00 pdb=" NE ARG C 303 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 303 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 303 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 303 " 0.126 9.50e-02 1.11e+02 5.66e-02 2.28e+00 pdb=" NE ARG D 303 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 303 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 303 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 303 " 0.001 2.00e-02 2.50e+03 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4764 2.78 - 3.31: 19184 3.31 - 3.84: 34701 3.84 - 4.37: 41817 4.37 - 4.90: 73958 Nonbonded interactions: 174424 Sorted by model distance: nonbonded pdb=" OE2 GLU D 31 " pdb=" NE2 HIS D 180 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU C 31 " pdb=" NE2 HIS C 180 " model vdw 2.255 3.120 nonbonded pdb=" OE2 GLU B 31 " pdb=" NE2 HIS B 180 " model vdw 2.255 3.120 nonbonded pdb=" OE2 GLU A 31 " pdb=" NE2 HIS A 180 " model vdw 2.261 3.120 nonbonded pdb=" OE2 GLU C 35 " pdb=" N GLY C 41 " model vdw 2.263 3.120 ... (remaining 174419 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 640 or resid 642)) selection = (chain 'B' and (resid 13 through 640 or resid 642)) selection = (chain 'C' and (resid 13 through 640 or resid 642)) selection = (chain 'D' and (resid 13 through 640 or resid 642)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.004 0.039 21720 Z= 0.156 Angle : 0.542 7.249 29426 Z= 0.276 Chirality : 0.041 0.163 3126 Planarity : 0.004 0.066 3802 Dihedral : 15.106 89.265 7884 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.13 % Allowed : 0.22 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2580 helix: 1.36 (0.15), residues: 1326 sheet: -0.39 (0.29), residues: 342 loop : -0.55 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 303 TYR 0.010 0.001 TYR A 623 PHE 0.014 0.002 PHE A 22 TRP 0.016 0.001 TRP A 134 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00379 (21720) covalent geometry : angle 0.54233 (29426) hydrogen bonds : bond 0.11556 ( 990) hydrogen bonds : angle 5.43560 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.948 Fit side-chains REVERT: A 237 GLN cc_start: 0.7732 (mp10) cc_final: 0.7424 (mp10) REVERT: A 448 MET cc_start: 0.8162 (mmp) cc_final: 0.7961 (mmp) REVERT: B 237 GLN cc_start: 0.7729 (mp10) cc_final: 0.7421 (mp10) REVERT: B 448 MET cc_start: 0.8198 (mmp) cc_final: 0.7943 (mmp) REVERT: C 237 GLN cc_start: 0.7738 (mp10) cc_final: 0.7427 (mp10) REVERT: C 448 MET cc_start: 0.8197 (mmp) cc_final: 0.7634 (mmp) REVERT: D 237 GLN cc_start: 0.7685 (mp10) cc_final: 0.7388 (mp10) REVERT: D 293 PHE cc_start: 0.7623 (m-80) cc_final: 0.7232 (m-80) REVERT: D 448 MET cc_start: 0.8193 (mmp) cc_final: 0.7944 (mmp) REVERT: E 336 ASP cc_start: 0.8142 (m-30) cc_final: 0.7934 (m-30) REVERT: F 336 ASP cc_start: 0.8154 (m-30) cc_final: 0.7921 (m-30) REVERT: G 336 ASP cc_start: 0.8179 (m-30) cc_final: 0.7948 (m-30) REVERT: H 336 ASP cc_start: 0.8156 (m-30) cc_final: 0.7929 (m-30) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.9256 time to fit residues: 268.0801 Evaluate side-chains 202 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 374 ASN D 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113629 restraints weight = 25788.713| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.69 r_work: 0.3142 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21720 Z= 0.123 Angle : 0.492 6.710 29426 Z= 0.257 Chirality : 0.040 0.147 3126 Planarity : 0.004 0.049 3802 Dihedral : 4.070 45.392 2884 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 6.71 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2580 helix: 1.75 (0.15), residues: 1344 sheet: -0.55 (0.28), residues: 352 loop : -0.31 (0.23), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 303 TYR 0.009 0.001 TYR A 623 PHE 0.012 0.001 PHE A 537 TRP 0.010 0.001 TRP B 134 HIS 0.003 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00293 (21720) covalent geometry : angle 0.49174 (29426) hydrogen bonds : bond 0.04115 ( 990) hydrogen bonds : angle 4.17323 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.745 Fit side-chains REVERT: A 237 GLN cc_start: 0.7972 (mp10) cc_final: 0.7606 (mp10) REVERT: A 264 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 448 MET cc_start: 0.8620 (mmp) cc_final: 0.8333 (mmp) REVERT: A 489 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6637 (mm) REVERT: B 237 GLN cc_start: 0.7944 (mp10) cc_final: 0.7593 (mp10) REVERT: B 264 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 489 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6623 (mm) REVERT: C 237 GLN cc_start: 0.7977 (mp10) cc_final: 0.7613 (mp10) REVERT: C 264 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8678 (mp) REVERT: C 282 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8872 (pp) REVERT: C 489 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6505 (mm) REVERT: D 237 GLN cc_start: 0.7912 (mp10) cc_final: 0.7689 (mp10) REVERT: D 264 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8677 (mp) REVERT: D 293 PHE cc_start: 0.7449 (m-80) cc_final: 0.6939 (m-80) REVERT: D 418 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7743 (ptmt) REVERT: D 489 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6614 (mm) REVERT: E 326 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7232 (mm-30) REVERT: G 326 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7263 (mm-30) REVERT: H 326 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7423 (mm-30) outliers start: 34 outliers final: 12 residues processed: 242 average time/residue: 0.8762 time to fit residues: 233.4087 Evaluate side-chains 218 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 205 optimal weight: 5.9990 chunk 27 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112167 restraints weight = 25888.382| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.72 r_work: 0.3100 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21720 Z= 0.134 Angle : 0.489 6.888 29426 Z= 0.254 Chirality : 0.041 0.147 3126 Planarity : 0.003 0.043 3802 Dihedral : 4.047 45.998 2884 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.73 % Allowed : 9.46 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2580 helix: 1.75 (0.14), residues: 1348 sheet: -0.56 (0.28), residues: 352 loop : -0.30 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 638 TYR 0.010 0.001 TYR C 623 PHE 0.013 0.001 PHE D 537 TRP 0.006 0.001 TRP F 325 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00327 (21720) covalent geometry : angle 0.48879 (29426) hydrogen bonds : bond 0.04051 ( 990) hydrogen bonds : angle 4.02213 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.823 Fit side-chains REVERT: A 237 GLN cc_start: 0.7862 (mp10) cc_final: 0.7658 (mm-40) REVERT: A 264 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 282 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8885 (pp) REVERT: A 448 MET cc_start: 0.8566 (mmp) cc_final: 0.8140 (mmp) REVERT: B 237 GLN cc_start: 0.7860 (mp10) cc_final: 0.7627 (mm-40) REVERT: B 264 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 282 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8873 (pp) REVERT: B 448 MET cc_start: 0.8552 (mmp) cc_final: 0.8185 (mmp) REVERT: B 489 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6673 (mm) REVERT: C 237 GLN cc_start: 0.7877 (mp10) cc_final: 0.7637 (mm-40) REVERT: C 264 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8656 (mp) REVERT: C 282 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8872 (pp) REVERT: C 418 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7811 (ptmt) REVERT: C 448 MET cc_start: 0.8570 (mmp) cc_final: 0.7880 (mmp) REVERT: C 489 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6650 (mm) REVERT: D 237 GLN cc_start: 0.7837 (mp10) cc_final: 0.7632 (mm-40) REVERT: D 264 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8664 (mp) REVERT: D 282 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 293 PHE cc_start: 0.7482 (m-80) cc_final: 0.7060 (m-80) REVERT: D 418 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7709 (ptmt) REVERT: D 448 MET cc_start: 0.8530 (mmp) cc_final: 0.8145 (mmp) REVERT: E 326 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7280 (mm-30) REVERT: F 322 LYS cc_start: 0.7093 (tttm) cc_final: 0.6856 (ttpp) REVERT: G 322 LYS cc_start: 0.6938 (tttm) cc_final: 0.6729 (ttpp) REVERT: H 326 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7310 (mm-30) outliers start: 39 outliers final: 11 residues processed: 227 average time/residue: 0.8832 time to fit residues: 220.5539 Evaluate side-chains 219 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 37 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 294 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 = 0.3671 r_free = 0.3671 target = 0.141043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113263 restraints weight = 25875.732| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.77 r_work: 0.3131 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21720 Z= 0.258 Angle : 0.610 7.447 29426 Z= 0.313 Chirality : 0.046 0.158 3126 Planarity : 0.005 0.047 3802 Dihedral : 4.333 40.387 2884 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.00 % Allowed : 12.34 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2580 helix: 1.46 (0.14), residues: 1340 sheet: -0.56 (0.29), residues: 348 loop : -0.44 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 638 TYR 0.010 0.002 TYR G 332 PHE 0.020 0.002 PHE C 22 TRP 0.015 0.002 TRP F 325 HIS 0.004 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00644 (21720) covalent geometry : angle 0.61035 (29426) hydrogen bonds : bond 0.05307 ( 990) hydrogen bonds : angle 4.26358 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.785 Fit side-chains REVERT: A 97 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7779 (mptt) REVERT: A 264 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 282 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9060 (pp) REVERT: A 418 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7882 (ptmt) REVERT: A 489 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6870 (mt) REVERT: B 264 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8826 (mp) REVERT: B 282 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9035 (pp) REVERT: B 294 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.5779 (mt0) REVERT: B 418 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7850 (ptmt) REVERT: B 448 MET cc_start: 0.8662 (mmp) cc_final: 0.8308 (mmp) REVERT: B 489 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6984 (mt) REVERT: C 97 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7787 (mptt) REVERT: C 264 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8817 (mp) REVERT: C 293 PHE cc_start: 0.7371 (m-80) cc_final: 0.6943 (m-80) REVERT: C 418 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7844 (ptmt) REVERT: C 489 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6901 (mt) REVERT: D 97 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7773 (mptt) REVERT: D 264 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8821 (mp) REVERT: D 282 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9019 (pp) REVERT: D 418 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7844 (ptmt) REVERT: D 448 MET cc_start: 0.8638 (mmp) cc_final: 0.8285 (mmp) REVERT: D 489 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6942 (mt) REVERT: E 326 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7198 (mm-30) REVERT: F 322 LYS cc_start: 0.7075 (tttm) cc_final: 0.6816 (ttpp) REVERT: G 322 LYS cc_start: 0.6984 (tttm) cc_final: 0.6708 (ttpp) REVERT: H 322 LYS cc_start: 0.6948 (tttm) cc_final: 0.6682 (ttpp) REVERT: H 326 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7344 (mm-30) outliers start: 45 outliers final: 15 residues processed: 225 average time/residue: 0.8984 time to fit residues: 222.2775 Evaluate side-chains 225 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 248 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3616 r_free = 0.3616 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113391 restraints weight = 25710.166| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.63 r_work: 0.3138 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21720 Z= 0.120 Angle : 0.484 7.072 29426 Z= 0.253 Chirality : 0.040 0.147 3126 Planarity : 0.003 0.047 3802 Dihedral : 4.127 47.136 2884 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.69 % Allowed : 13.72 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2580 helix: 1.73 (0.14), residues: 1348 sheet: -0.61 (0.28), residues: 352 loop : -0.35 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 303 TYR 0.009 0.001 TYR A 623 PHE 0.012 0.001 PHE B 537 TRP 0.008 0.001 TRP E 325 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00291 (21720) covalent geometry : angle 0.48364 (29426) hydrogen bonds : bond 0.03960 ( 990) hydrogen bonds : angle 3.97281 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.810 Fit side-chains REVERT: A 264 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 294 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5684 (mt0) REVERT: A 489 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6861 (mm) REVERT: B 264 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 418 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7721 (ptmt) REVERT: B 448 MET cc_start: 0.8581 (mmp) cc_final: 0.8335 (mmp) REVERT: B 489 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6780 (mm) REVERT: C 264 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (mp) REVERT: C 293 PHE cc_start: 0.7409 (m-80) cc_final: 0.7021 (m-80) REVERT: C 294 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5669 (mt0) REVERT: C 418 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7769 (ptmt) REVERT: C 489 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6754 (mm) REVERT: D 264 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8642 (mp) REVERT: D 418 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7721 (ptmt) REVERT: D 448 MET cc_start: 0.8572 (mmp) cc_final: 0.8335 (mmp) REVERT: D 489 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6780 (mm) REVERT: E 326 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7237 (mm-30) REVERT: G 322 LYS cc_start: 0.7090 (tttm) cc_final: 0.6828 (ttpp) REVERT: H 322 LYS cc_start: 0.7122 (tttm) cc_final: 0.6892 (ttpp) REVERT: H 326 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7358 (mm-30) outliers start: 38 outliers final: 16 residues processed: 227 average time/residue: 0.8878 time to fit residues: 221.6034 Evaluate side-chains 216 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain E residue 336 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 88 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3721 r_free = 0.3721 target = 0.144952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116625 restraints weight = 25512.870| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.80 r_work: 0.3153 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21720 Z= 0.150 Angle : 0.514 8.262 29426 Z= 0.265 Chirality : 0.041 0.147 3126 Planarity : 0.004 0.081 3802 Dihedral : 4.138 47.247 2884 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.18 % Allowed : 13.81 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2580 helix: 1.71 (0.14), residues: 1348 sheet: -0.59 (0.28), residues: 352 loop : -0.36 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 303 TYR 0.008 0.001 TYR D 623 PHE 0.014 0.001 PHE A 537 TRP 0.011 0.001 TRP F 325 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00372 (21720) covalent geometry : angle 0.51424 (29426) hydrogen bonds : bond 0.04196 ( 990) hydrogen bonds : angle 3.97018 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.742 Fit side-chains REVERT: A 264 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 294 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.5653 (mt0) REVERT: B 36 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8700 (t) REVERT: B 264 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 294 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5858 (mt0) REVERT: B 418 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7777 (ptmt) REVERT: B 489 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6996 (mt) REVERT: C 36 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8688 (t) REVERT: C 264 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (mp) REVERT: C 293 PHE cc_start: 0.7410 (m-80) cc_final: 0.7002 (m-80) REVERT: C 294 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5560 (mt0) REVERT: C 418 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7784 (ptmt) REVERT: C 489 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6906 (mt) REVERT: D 36 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8700 (t) REVERT: D 264 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 293 PHE cc_start: 0.7599 (m-80) cc_final: 0.7334 (m-80) REVERT: D 418 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7761 (ptmt) REVERT: E 326 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7242 (mm-30) REVERT: H 322 LYS cc_start: 0.7045 (tttm) cc_final: 0.6788 (ttpp) REVERT: H 326 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7383 (mm-30) outliers start: 49 outliers final: 19 residues processed: 228 average time/residue: 0.8156 time to fit residues: 205.2203 Evaluate side-chains 222 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 139 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.2980 chunk 213 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3622 r_free = 0.3622 target = 0.140336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113226 restraints weight = 25603.806| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.72 r_work: 0.3131 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21720 Z= 0.105 Angle : 0.472 8.024 29426 Z= 0.244 Chirality : 0.040 0.146 3126 Planarity : 0.004 0.066 3802 Dihedral : 4.001 51.057 2884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.17), residues: 2580 helix: 1.90 (0.14), residues: 1344 sheet: -0.56 (0.29), residues: 344 loop : -0.26 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 303 TYR 0.009 0.001 TYR A 623 PHE 0.010 0.001 PHE D 537 TRP 0.013 0.001 TRP C 134 HIS 0.003 0.000 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00256 (21720) covalent geometry : angle 0.47232 (29426) hydrogen bonds : bond 0.03577 ( 990) hydrogen bonds : angle 3.80473 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.848 Fit side-chains REVERT: A 264 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 294 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5722 (mt0) REVERT: B 264 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 294 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5839 (mt0) REVERT: B 418 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7657 (ptmt) REVERT: B 489 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6767 (mm) REVERT: C 264 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 293 PHE cc_start: 0.7340 (m-80) cc_final: 0.6972 (m-80) REVERT: C 294 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5599 (mt0) REVERT: C 418 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7720 (ptmt) REVERT: C 489 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6650 (mm) REVERT: D 264 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D 293 PHE cc_start: 0.7552 (m-80) cc_final: 0.7308 (m-80) REVERT: D 418 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7688 (ptmt) REVERT: E 326 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7200 (mm-30) REVERT: H 326 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7273 (mm-30) outliers start: 32 outliers final: 13 residues processed: 220 average time/residue: 0.8901 time to fit residues: 215.4122 Evaluate side-chains 212 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3686 r_free = 0.3686 target = 0.142334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113904 restraints weight = 25659.303| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.81 r_work: 0.3140 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21720 Z= 0.190 Angle : 0.554 9.172 29426 Z= 0.281 Chirality : 0.043 0.147 3126 Planarity : 0.005 0.090 3802 Dihedral : 4.169 46.423 2884 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.95 % Allowed : 14.30 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2580 helix: 1.75 (0.14), residues: 1332 sheet: -0.53 (0.29), residues: 346 loop : -0.28 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 303 TYR 0.009 0.001 TYR B 44 PHE 0.016 0.002 PHE A 537 TRP 0.018 0.002 TRP G 325 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00472 (21720) covalent geometry : angle 0.55415 (29426) hydrogen bonds : bond 0.04528 ( 990) hydrogen bonds : angle 3.97643 ( 2931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.947 Fit side-chains REVERT: A 264 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 294 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.5727 (mt0) REVERT: A 418 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7753 (ptmt) REVERT: A 448 MET cc_start: 0.8680 (mmp) cc_final: 0.8308 (mmp) REVERT: B 264 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8649 (mp) REVERT: B 294 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.5932 (mt0) REVERT: B 418 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (ptmt) REVERT: B 489 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6837 (mt) REVERT: C 264 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 293 PHE cc_start: 0.7446 (m-80) cc_final: 0.7095 (m-80) REVERT: C 294 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5547 (mt0) REVERT: C 418 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7735 (ptmt) REVERT: C 489 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6775 (mt) REVERT: D 264 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8632 (mp) REVERT: D 418 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7718 (ptmt) REVERT: E 322 LYS cc_start: 0.7052 (tttm) cc_final: 0.6816 (ttpp) outliers start: 44 outliers final: 15 residues processed: 219 average time/residue: 0.8908 time to fit residues: 215.0296 Evaluate side-chains 219 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 130 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3735 r_free = 0.3735 target = 0.146054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117701 restraints weight = 25333.543| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.81 r_work: 0.3171 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21720 Z= 0.125 Angle : 0.508 9.880 29426 Z= 0.258 Chirality : 0.041 0.147 3126 Planarity : 0.004 0.083 3802 Dihedral : 4.086 50.036 2884 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.55 % Allowed : 14.65 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2580 helix: 1.94 (0.14), residues: 1320 sheet: -0.55 (0.29), residues: 346 loop : -0.24 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 303 TYR 0.007 0.001 TYR A 623 PHE 0.012 0.001 PHE A 537 TRP 0.020 0.001 TRP D 134 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00310 (21720) covalent geometry : angle 0.50775 (29426) hydrogen bonds : bond 0.03870 ( 990) hydrogen bonds : angle 3.83236 ( 2931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.593 Fit side-chains REVERT: A 264 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 294 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.5617 (mt0) REVERT: B 264 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8515 (mp) REVERT: B 294 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5797 (mt0) REVERT: B 418 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7687 (ptmt) REVERT: B 448 MET cc_start: 0.8543 (mmp) cc_final: 0.8176 (mmp) REVERT: B 489 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6860 (mt) REVERT: C 264 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 293 PHE cc_start: 0.7382 (m-80) cc_final: 0.6959 (m-80) REVERT: C 294 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5535 (mt0) REVERT: C 418 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7616 (ptmt) REVERT: D 264 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8489 (mp) REVERT: D 418 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7589 (ptmt) REVERT: D 448 MET cc_start: 0.8529 (mmp) cc_final: 0.8179 (mmp) REVERT: E 322 LYS cc_start: 0.7105 (tttm) cc_final: 0.6844 (ttpp) REVERT: F 322 LYS cc_start: 0.7134 (tttm) cc_final: 0.6910 (ttpp) REVERT: G 336 ASP cc_start: 0.8155 (m-30) cc_final: 0.7850 (t0) REVERT: H 336 ASP cc_start: 0.8160 (m-30) cc_final: 0.7849 (t0) outliers start: 35 outliers final: 14 residues processed: 227 average time/residue: 0.8737 time to fit residues: 217.9359 Evaluate side-chains 222 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 186 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 228 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 235 optimal weight: 0.0060 chunk 14 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3753 r_free = 0.3753 target = 0.147474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119286 restraints weight = 25368.086| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.81 r_work: 0.3196 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21720 Z= 0.105 Angle : 0.497 10.356 29426 Z= 0.252 Chirality : 0.040 0.146 3126 Planarity : 0.004 0.071 3802 Dihedral : 4.007 52.810 2884 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 15.23 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2580 helix: 2.08 (0.15), residues: 1316 sheet: -0.53 (0.29), residues: 344 loop : -0.22 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 303 TYR 0.007 0.001 TYR A 623 PHE 0.010 0.001 PHE B 537 TRP 0.026 0.001 TRP C 134 HIS 0.002 0.000 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00255 (21720) covalent geometry : angle 0.49660 (29426) hydrogen bonds : bond 0.03505 ( 990) hydrogen bonds : angle 3.73832 ( 2931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.828 Fit side-chains REVERT: A 264 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 294 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5546 (mt0) REVERT: A 448 MET cc_start: 0.8520 (mmp) cc_final: 0.8060 (mmp) REVERT: B 264 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8383 (mp) REVERT: B 294 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5712 (mt0) REVERT: B 489 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6670 (mm) REVERT: C 264 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 293 PHE cc_start: 0.7341 (m-80) cc_final: 0.6870 (m-80) REVERT: C 294 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5498 (mt0) REVERT: C 418 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7606 (ptmt) REVERT: D 264 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 293 PHE cc_start: 0.7529 (m-80) cc_final: 0.7277 (m-80) REVERT: D 418 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7546 (ptmt) REVERT: E 322 LYS cc_start: 0.7111 (tttm) cc_final: 0.6876 (ttpp) REVERT: F 322 LYS cc_start: 0.7187 (tttm) cc_final: 0.6958 (ttpp) REVERT: F 336 ASP cc_start: 0.8137 (m-30) cc_final: 0.7859 (t0) REVERT: G 322 LYS cc_start: 0.7171 (tttm) cc_final: 0.6942 (ttpp) REVERT: G 336 ASP cc_start: 0.8169 (m-30) cc_final: 0.7905 (t0) REVERT: H 336 ASP cc_start: 0.8162 (m-30) cc_final: 0.7911 (t0) outliers start: 28 outliers final: 14 residues processed: 229 average time/residue: 0.8414 time to fit residues: 212.9787 Evaluate side-chains 222 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 162 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 187 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 233 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 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 = 0.3704 r_free = 0.3704 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115184 restraints weight = 25744.490| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.92 r_work: 0.3149 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21720 Z= 0.105 Angle : 0.485 10.457 29426 Z= 0.246 Chirality : 0.040 0.147 3126 Planarity : 0.003 0.048 3802 Dihedral : 3.950 52.318 2884 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.20 % Allowed : 15.59 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2580 helix: 2.06 (0.14), residues: 1316 sheet: -0.52 (0.29), residues: 344 loop : -0.19 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 580 TYR 0.007 0.001 TYR B 623 PHE 0.010 0.001 PHE B 537 TRP 0.031 0.001 TRP D 134 HIS 0.003 0.000 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00256 (21720) covalent geometry : angle 0.48518 (29426) hydrogen bonds : bond 0.03550 ( 990) hydrogen bonds : angle 3.75316 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6660.23 seconds wall clock time: 114 minutes 21.61 seconds (6861.61 seconds total)