Starting phenix.real_space_refine on Sat Oct 11 11:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.map" model { file = "/net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p7w_17537/10_2025/8p7w_17537.cif" } resolution = 3.04 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= 0.001 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9232 2.51 5 N 2392 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14380 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Y" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 3.27, per 1000 atoms: 0.23 Number of scatterers: 14380 At special positions: 0 Unit cell: (93.24, 91.56, 183.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2678 8.00 N 2392 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 50 " - pdb=" SG CYS Y 106 " distance=2.03 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: 1.15 Conformation dependent library (CDL) restraints added in 680.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 38.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.906A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.619A pdb=" N PHE A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.518A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.050A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.837A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.651A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.580A pdb=" N LEU A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.556A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.825A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 removed outlier: 3.898A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.615A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.621A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.724A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 3.844A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.514A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.699A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.541A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 5.076A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.904A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.617A pdb=" N PHE B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.500A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.534A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.036A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 4.098A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.654A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.630A pdb=" N LEU B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.576A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.823A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 removed outlier: 3.819A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.595A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.600A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 476 removed outlier: 3.727A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.867A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 502 through 528 removed outlier: 3.684A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.574A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.073A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.107A pdb=" N TYR C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.046A pdb=" N TYR Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 71 removed outlier: 5.560A pdb=" N SER A 65 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY A 69 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS A 40 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 71 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER A 38 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.386A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.080A pdb=" N ARG A 309 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 71 removed outlier: 5.473A pdb=" N SER B 65 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY B 69 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS B 40 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET B 71 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER B 38 " --> pdb=" O MET B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.375A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.813A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.458A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 48 removed outlier: 6.421A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER Y 71 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 46 through 49 removed outlier: 7.078A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1746 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: 2.50 Time building geometry restraints manager: 1.47 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: 4530 1.34 - 1.46: 3605 1.46 - 1.58: 6445 1.58 - 1.70: 0 1.70 - 1.81: 118 Bond restraints: 14698 Sorted by residual: bond pdb=" CG PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.04e+00 bond pdb=" C CYS A 592 " pdb=" O CYS A 592 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.87e+00 bond pdb=" C CYS B 592 " pdb=" O CYS B 592 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.81e+00 bond pdb=" CA ARG C 67 " pdb=" CB ARG C 67 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.51e-02 4.39e+03 1.69e+00 bond pdb=" CG1 ILE B 412 " pdb=" CD1 ILE B 412 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 ... (remaining 14693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 19635 2.40 - 4.79: 241 4.79 - 7.19: 36 7.19 - 9.58: 1 9.58 - 11.98: 3 Bond angle restraints: 19916 Sorted by residual: angle pdb=" N GLU B 458 " pdb=" CA GLU B 458 " pdb=" CB GLU B 458 " ideal model delta sigma weight residual 110.12 115.83 -5.71 1.47e+00 4.63e-01 1.51e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.42e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" CB MET Y 83 " pdb=" CG MET Y 83 " pdb=" SD MET Y 83 " ideal model delta sigma weight residual 112.70 123.85 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C TYR D 60 " pdb=" N ASN D 61 " pdb=" CA ASN D 61 " ideal model delta sigma weight residual 120.49 125.58 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 19911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7471 17.71 - 35.42: 950 35.42 - 53.14: 191 53.14 - 70.85: 29 70.85 - 88.56: 16 Dihedral angle restraints: 8657 sinusoidal: 3355 harmonic: 5302 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 138.05 -45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS Y 50 " pdb=" SG CYS Y 50 " pdb=" SG CYS Y 106 " pdb=" CB CYS Y 106 " ideal model delta sinusoidal sigma weight residual 93.00 54.71 38.29 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS C 50 " pdb=" SG CYS C 50 " pdb=" SG CYS C 106 " pdb=" CB CYS C 106 " ideal model delta sinusoidal sigma weight residual 93.00 57.95 35.05 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 8654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1222 0.029 - 0.058: 701 0.058 - 0.087: 216 0.087 - 0.116: 80 0.116 - 0.145: 29 Chirality restraints: 2248 Sorted by residual: chirality pdb=" CA ILE Y 51 " pdb=" N ILE Y 51 " pdb=" C ILE Y 51 " pdb=" CB ILE Y 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA LEU B 140 " pdb=" N LEU B 140 " pdb=" C LEU B 140 " pdb=" CB LEU B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2245 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO D 88 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 90 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASP F 90 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP F 90 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 91 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 68 " 0.013 2.00e-02 2.50e+03 1.41e-02 3.46e+00 pdb=" CG PHE C 68 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 68 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 68 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 68 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 68 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 68 " 0.000 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1494 2.74 - 3.28: 13842 3.28 - 3.82: 23824 3.82 - 4.36: 27027 4.36 - 4.90: 48398 Nonbonded interactions: 114585 Sorted by model distance: nonbonded pdb=" OG1 THR D 23 " pdb=" OE1 GLN D 78 " model vdw 2.206 3.040 nonbonded pdb=" O ASN C 103 " pdb=" OH TYR C 109 " model vdw 2.217 3.040 nonbonded pdb=" O LEU C 11 " pdb=" OG1 THR C 121 " model vdw 2.219 3.040 nonbonded pdb=" O SER G 77 " pdb=" OG SER G 77 " model vdw 2.221 3.040 nonbonded pdb=" O ASN Y 103 " pdb=" OH TYR Y 109 " model vdw 2.229 3.040 ... (remaining 114580 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 0.053 14709 Z= 0.182 Angle : 0.723 11.978 19938 Z= 0.424 Chirality : 0.042 0.145 2248 Planarity : 0.004 0.101 2508 Dihedral : 15.985 88.560 5248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.45 % Allowed : 23.09 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.20), residues: 1824 helix: 1.05 (0.21), residues: 652 sheet: -1.48 (0.24), residues: 390 loop : -2.46 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 101 TYR 0.012 0.001 TYR B 463 PHE 0.032 0.001 PHE C 68 TRP 0.023 0.001 TRP Y 36 HIS 0.009 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00381 (14698) covalent geometry : angle 0.72253 (19916) SS BOND : bond 0.00345 ( 11) SS BOND : angle 1.12501 ( 22) hydrogen bonds : bond 0.16552 ( 627) hydrogen bonds : angle 5.68047 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 382 time to evaluate : 0.559 Fit side-chains REVERT: B 393 GLN cc_start: 0.7833 (pp30) cc_final: 0.7587 (mt0) REVERT: B 481 MET cc_start: 0.8443 (tpp) cc_final: 0.8227 (mmm) REVERT: D 77 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7804 (t0) REVERT: D 78 GLN cc_start: 0.8200 (mt0) cc_final: 0.7522 (mp10) REVERT: F 13 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7203 (ptmm) REVERT: F 70 ILE cc_start: 0.8305 (mm) cc_final: 0.8076 (mt) REVERT: F 77 ASN cc_start: 0.8889 (t0) cc_final: 0.8646 (t0) REVERT: F 111 GLN cc_start: 0.7305 (mp10) cc_final: 0.7081 (mp10) REVERT: G 17 ASP cc_start: 0.7813 (m-30) cc_final: 0.7431 (m-30) outliers start: 7 outliers final: 1 residues processed: 385 average time/residue: 0.1284 time to fit residues: 71.6851 Evaluate side-chains 359 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain D residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 283 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN G 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106024 restraints weight = 20196.418| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.74 r_work: 0.3139 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14709 Z= 0.195 Angle : 0.588 8.417 19938 Z= 0.305 Chirality : 0.042 0.161 2248 Planarity : 0.004 0.071 2508 Dihedral : 4.062 34.039 2004 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.01 % Allowed : 19.78 % Favored : 76.21 % 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 aren not related in a simple way. whole: -1.16 (0.20), residues: 1824 helix: 1.45 (0.21), residues: 652 sheet: -1.38 (0.25), residues: 376 loop : -2.42 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 101 TYR 0.020 0.002 TYR B 463 PHE 0.020 0.002 PHE A 293 TRP 0.016 0.001 TRP Y 36 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00454 (14698) covalent geometry : angle 0.58668 (19916) SS BOND : bond 0.00405 ( 11) SS BOND : angle 1.32835 ( 22) hydrogen bonds : bond 0.04529 ( 627) hydrogen bonds : angle 4.53665 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 370 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 541 MET cc_start: 0.8422 (mtm) cc_final: 0.8041 (mtm) REVERT: B 292 ASP cc_start: 0.8828 (m-30) cc_final: 0.8616 (m-30) REVERT: B 311 GLU cc_start: 0.7466 (mp0) cc_final: 0.7067 (mp0) REVERT: B 398 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 402 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8448 (t) REVERT: B 417 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8553 (mttm) REVERT: D 95 TYR cc_start: 0.8522 (m-80) cc_final: 0.8113 (m-80) REVERT: D 107 ASP cc_start: 0.8869 (m-30) cc_final: 0.8580 (m-30) REVERT: E 11 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: F 78 GLN cc_start: 0.7810 (pt0) cc_final: 0.7386 (pm20) REVERT: G 17 ASP cc_start: 0.7839 (m-30) cc_final: 0.7468 (m-30) REVERT: Y 77 ASN cc_start: 0.8444 (t0) cc_final: 0.8227 (t0) outliers start: 63 outliers final: 34 residues processed: 401 average time/residue: 0.1275 time to fit residues: 74.5687 Evaluate side-chains 381 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 0.0470 chunk 155 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN E 6 GLN F 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106775 restraints weight = 20237.718| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.73 r_work: 0.3155 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14709 Z= 0.144 Angle : 0.543 7.965 19938 Z= 0.280 Chirality : 0.040 0.143 2248 Planarity : 0.004 0.063 2508 Dihedral : 3.869 20.371 2000 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.33 % Allowed : 19.97 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1824 helix: 1.68 (0.21), residues: 652 sheet: -1.14 (0.27), residues: 340 loop : -2.32 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 101 TYR 0.015 0.001 TYR B 463 PHE 0.021 0.001 PHE Y 68 TRP 0.010 0.001 TRP F 35 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00337 (14698) covalent geometry : angle 0.54252 (19916) SS BOND : bond 0.00320 ( 11) SS BOND : angle 1.10512 ( 22) hydrogen bonds : bond 0.03979 ( 627) hydrogen bonds : angle 4.26040 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 292 ASP cc_start: 0.8816 (m-30) cc_final: 0.8562 (m-30) REVERT: A 398 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7406 (mp-120) REVERT: A 402 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8468 (t) REVERT: B 292 ASP cc_start: 0.8787 (m-30) cc_final: 0.8559 (m-30) REVERT: B 398 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 402 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8486 (t) REVERT: B 417 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8496 (mttm) REVERT: C 73 ASP cc_start: 0.8593 (t0) cc_final: 0.8381 (t0) REVERT: D 72 ARG cc_start: 0.8861 (ptt180) cc_final: 0.8656 (ptt180) REVERT: D 77 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (t0) REVERT: D 95 TYR cc_start: 0.8490 (m-80) cc_final: 0.8054 (m-80) REVERT: D 107 ASP cc_start: 0.8930 (m-30) cc_final: 0.8646 (m-30) REVERT: E 11 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: F 13 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7317 (ptmm) REVERT: F 70 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8247 (mm) REVERT: F 78 GLN cc_start: 0.7905 (pt0) cc_final: 0.7483 (pm20) REVERT: G 17 ASP cc_start: 0.7921 (m-30) cc_final: 0.7566 (m-30) REVERT: Y 73 ASP cc_start: 0.8633 (t0) cc_final: 0.8286 (t0) REVERT: Y 77 ASN cc_start: 0.8456 (t0) cc_final: 0.8242 (t0) outliers start: 68 outliers final: 42 residues processed: 405 average time/residue: 0.1290 time to fit residues: 76.0388 Evaluate side-chains 400 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 154 optimal weight: 0.0470 chunk 162 optimal weight: 0.0030 chunk 156 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106571 restraints weight = 20031.028| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.74 r_work: 0.3153 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.142 Angle : 0.541 7.406 19938 Z= 0.278 Chirality : 0.040 0.146 2248 Planarity : 0.004 0.058 2508 Dihedral : 3.839 20.575 2000 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.90 % Allowed : 19.85 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1824 helix: 1.80 (0.21), residues: 652 sheet: -1.03 (0.27), residues: 340 loop : -2.25 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 101 TYR 0.018 0.001 TYR B 463 PHE 0.016 0.001 PHE A 293 TRP 0.008 0.001 TRP F 35 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00335 (14698) covalent geometry : angle 0.54051 (19916) SS BOND : bond 0.00321 ( 11) SS BOND : angle 1.05849 ( 22) hydrogen bonds : bond 0.03825 ( 627) hydrogen bonds : angle 4.16274 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 373 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8742 (m110) cc_final: 0.8146 (t0) REVERT: A 292 ASP cc_start: 0.8753 (m-30) cc_final: 0.8503 (m-30) REVERT: A 398 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7387 (mp-120) REVERT: A 402 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8458 (t) REVERT: B 292 ASP cc_start: 0.8761 (m-30) cc_final: 0.8545 (m-30) REVERT: B 398 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: B 402 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 417 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8540 (mttm) REVERT: C 73 ASP cc_start: 0.8541 (t0) cc_final: 0.8319 (t0) REVERT: D 72 ARG cc_start: 0.8869 (ptt180) cc_final: 0.8665 (ptt180) REVERT: D 78 GLN cc_start: 0.8295 (mt0) cc_final: 0.7427 (mp10) REVERT: D 107 ASP cc_start: 0.8943 (m-30) cc_final: 0.8672 (m-30) REVERT: E 11 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: F 13 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7381 (ptmm) REVERT: F 70 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8189 (mm) REVERT: F 78 GLN cc_start: 0.7898 (pt0) cc_final: 0.7432 (pm20) REVERT: G 17 ASP cc_start: 0.7975 (m-30) cc_final: 0.7627 (m-30) REVERT: Y 73 ASP cc_start: 0.8660 (t0) cc_final: 0.8413 (t0) REVERT: Y 77 ASN cc_start: 0.8416 (t0) cc_final: 0.8179 (t0) outliers start: 77 outliers final: 49 residues processed: 411 average time/residue: 0.1296 time to fit residues: 77.5536 Evaluate side-chains 413 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104160 restraints weight = 20134.353| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.72 r_work: 0.3121 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14709 Z= 0.185 Angle : 0.573 9.673 19938 Z= 0.294 Chirality : 0.041 0.159 2248 Planarity : 0.004 0.055 2508 Dihedral : 3.934 20.455 2000 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 5.92 % Allowed : 19.72 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1824 helix: 1.77 (0.21), residues: 652 sheet: -0.91 (0.26), residues: 360 loop : -2.29 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 101 TYR 0.013 0.001 TYR B 463 PHE 0.017 0.001 PHE A 293 TRP 0.006 0.001 TRP Y 36 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00435 (14698) covalent geometry : angle 0.57260 (19916) SS BOND : bond 0.00391 ( 11) SS BOND : angle 1.12360 ( 22) hydrogen bonds : bond 0.04162 ( 627) hydrogen bonds : angle 4.12209 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 378 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8756 (m110) cc_final: 0.8154 (t0) REVERT: A 148 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 217 ASP cc_start: 0.8245 (p0) cc_final: 0.8039 (p0) REVERT: A 292 ASP cc_start: 0.8744 (m-30) cc_final: 0.8491 (m-30) REVERT: A 398 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7295 (mp-120) REVERT: A 402 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8483 (t) REVERT: B 292 ASP cc_start: 0.8755 (m-30) cc_final: 0.8551 (m-30) REVERT: B 398 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: B 402 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8493 (t) REVERT: B 417 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8485 (mttm) REVERT: C 73 ASP cc_start: 0.8619 (t0) cc_final: 0.8378 (t0) REVERT: D 78 GLN cc_start: 0.8321 (mt0) cc_final: 0.7504 (mp10) REVERT: D 81 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7912 (tp) REVERT: D 107 ASP cc_start: 0.8945 (m-30) cc_final: 0.8689 (m-30) REVERT: E 11 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: E 24 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6530 (mtmm) REVERT: F 70 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8208 (mm) REVERT: F 78 GLN cc_start: 0.7936 (pt0) cc_final: 0.7435 (pm20) REVERT: G 17 ASP cc_start: 0.8013 (m-30) cc_final: 0.7662 (m-30) REVERT: Y 73 ASP cc_start: 0.8690 (t0) cc_final: 0.8457 (t0) REVERT: Y 77 ASN cc_start: 0.8393 (t0) cc_final: 0.8153 (t0) outliers start: 93 outliers final: 61 residues processed: 420 average time/residue: 0.1249 time to fit residues: 77.1408 Evaluate side-chains 434 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 chunk 120 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** B 391 ASN ** 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 = 0.3718 r_free = 0.3718 target = 0.141146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107658 restraints weight = 19903.084| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.73 r_work: 0.3168 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14709 Z= 0.114 Angle : 0.546 8.418 19938 Z= 0.275 Chirality : 0.040 0.134 2248 Planarity : 0.004 0.053 2508 Dihedral : 3.767 21.064 2000 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.39 % Allowed : 21.69 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.20), residues: 1824 helix: 2.09 (0.21), residues: 636 sheet: -0.72 (0.27), residues: 356 loop : -2.21 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 101 TYR 0.016 0.001 TYR B 463 PHE 0.015 0.001 PHE A 293 TRP 0.012 0.001 TRP F 35 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00269 (14698) covalent geometry : angle 0.54495 (19916) SS BOND : bond 0.00268 ( 11) SS BOND : angle 0.93542 ( 22) hydrogen bonds : bond 0.03450 ( 627) hydrogen bonds : angle 3.99678 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 389 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8682 (m110) cc_final: 0.7899 (t0) REVERT: A 292 ASP cc_start: 0.8713 (m-30) cc_final: 0.8491 (m-30) REVERT: A 398 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: A 446 GLU cc_start: 0.8763 (mp0) cc_final: 0.8122 (mp0) REVERT: B 43 CYS cc_start: 0.6934 (m) cc_final: 0.6478 (m) REVERT: B 105 ASP cc_start: 0.7920 (t70) cc_final: 0.7700 (t70) REVERT: B 292 ASP cc_start: 0.8737 (m-30) cc_final: 0.8526 (m-30) REVERT: B 398 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: B 417 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8486 (mttm) REVERT: B 446 GLU cc_start: 0.8768 (mp0) cc_final: 0.8140 (mp0) REVERT: C 73 ASP cc_start: 0.8584 (t0) cc_final: 0.8332 (t0) REVERT: D 78 GLN cc_start: 0.8294 (mt0) cc_final: 0.7506 (mp10) REVERT: D 81 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7949 (tp) REVERT: D 107 ASP cc_start: 0.8928 (m-30) cc_final: 0.8706 (m-30) REVERT: E 11 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: E 24 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6469 (mtmm) REVERT: F 13 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7328 (ptmm) REVERT: F 78 GLN cc_start: 0.7878 (pt0) cc_final: 0.7393 (pm20) REVERT: G 17 ASP cc_start: 0.8017 (m-30) cc_final: 0.7684 (m-30) REVERT: Y 73 ASP cc_start: 0.8694 (t0) cc_final: 0.8455 (t0) outliers start: 69 outliers final: 45 residues processed: 422 average time/residue: 0.1267 time to fit residues: 78.2312 Evaluate side-chains 425 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Y 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106987 restraints weight = 19972.758| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.73 r_work: 0.3159 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14709 Z= 0.131 Angle : 0.556 8.605 19938 Z= 0.282 Chirality : 0.040 0.177 2248 Planarity : 0.004 0.053 2508 Dihedral : 3.754 20.908 2000 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.52 % Allowed : 22.01 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.20), residues: 1824 helix: 2.11 (0.21), residues: 636 sheet: -0.68 (0.27), residues: 356 loop : -2.14 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 101 TYR 0.018 0.001 TYR B 463 PHE 0.015 0.001 PHE A 293 TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00311 (14698) covalent geometry : angle 0.55504 (19916) SS BOND : bond 0.00303 ( 11) SS BOND : angle 1.05362 ( 22) hydrogen bonds : bond 0.03587 ( 627) hydrogen bonds : angle 3.92055 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 379 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8691 (m110) cc_final: 0.8105 (t0) REVERT: A 398 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: A 502 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8865 (mmtm) REVERT: B 43 CYS cc_start: 0.7070 (m) cc_final: 0.6523 (m) REVERT: B 398 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: B 446 GLU cc_start: 0.8758 (mp0) cc_final: 0.8112 (mp0) REVERT: C 73 ASP cc_start: 0.8599 (t0) cc_final: 0.8337 (t0) REVERT: D 13 LYS cc_start: 0.7622 (mtpp) cc_final: 0.7222 (ptmm) REVERT: D 78 GLN cc_start: 0.8289 (mt0) cc_final: 0.7501 (mp10) REVERT: D 81 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8014 (tp) REVERT: D 107 ASP cc_start: 0.8937 (m-30) cc_final: 0.8728 (m-30) REVERT: E 11 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: F 13 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7373 (ptmm) REVERT: F 78 GLN cc_start: 0.7968 (pt0) cc_final: 0.7513 (pm20) REVERT: G 17 ASP cc_start: 0.8007 (m-30) cc_final: 0.7681 (m-30) REVERT: Y 73 ASP cc_start: 0.8725 (t0) cc_final: 0.8482 (t0) outliers start: 71 outliers final: 53 residues processed: 414 average time/residue: 0.1218 time to fit residues: 73.6785 Evaluate side-chains 431 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 27 optimal weight: 0.3980 chunk 156 optimal weight: 4.9990 chunk 137 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109126 restraints weight = 19832.014| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.74 r_work: 0.3185 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14709 Z= 0.110 Angle : 0.546 8.849 19938 Z= 0.276 Chirality : 0.040 0.199 2248 Planarity : 0.004 0.051 2508 Dihedral : 3.670 20.731 2000 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.88 % Allowed : 22.65 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1824 helix: 2.13 (0.21), residues: 636 sheet: -0.49 (0.27), residues: 372 loop : -2.09 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 101 TYR 0.019 0.001 TYR B 463 PHE 0.015 0.001 PHE B 293 TRP 0.012 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00258 (14698) covalent geometry : angle 0.54515 (19916) SS BOND : bond 0.00254 ( 11) SS BOND : angle 1.04022 ( 22) hydrogen bonds : bond 0.03264 ( 627) hydrogen bonds : angle 3.83228 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8663 (m110) cc_final: 0.7870 (t0) REVERT: A 458 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 43 CYS cc_start: 0.6740 (m) cc_final: 0.6310 (m) REVERT: B 398 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: B 446 GLU cc_start: 0.8767 (mp0) cc_final: 0.8110 (mp0) REVERT: C 73 ASP cc_start: 0.8614 (t0) cc_final: 0.8336 (t0) REVERT: D 13 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7193 (ptmm) REVERT: D 78 GLN cc_start: 0.8273 (mt0) cc_final: 0.7479 (mp10) REVERT: D 81 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8047 (tp) REVERT: E 11 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: F 13 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7385 (ptmm) REVERT: F 78 GLN cc_start: 0.7935 (pt0) cc_final: 0.7470 (pm20) REVERT: F 82 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7515 (tm-30) REVERT: G 17 ASP cc_start: 0.7963 (m-30) cc_final: 0.7654 (m-30) REVERT: Y 73 ASP cc_start: 0.8734 (t0) cc_final: 0.8373 (t0) outliers start: 61 outliers final: 50 residues processed: 418 average time/residue: 0.1253 time to fit residues: 76.0033 Evaluate side-chains 430 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103729 restraints weight = 20168.953| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.72 r_work: 0.3112 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14709 Z= 0.208 Angle : 0.625 12.553 19938 Z= 0.317 Chirality : 0.043 0.232 2248 Planarity : 0.004 0.052 2508 Dihedral : 3.953 21.493 2000 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.07 % Allowed : 23.16 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1824 helix: 2.03 (0.21), residues: 636 sheet: -0.55 (0.26), residues: 392 loop : -2.12 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 101 TYR 0.017 0.002 TYR B 463 PHE 0.017 0.002 PHE A 293 TRP 0.011 0.001 TRP F 37 HIS 0.004 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00492 (14698) covalent geometry : angle 0.62376 (19916) SS BOND : bond 0.00418 ( 11) SS BOND : angle 1.32439 ( 22) hydrogen bonds : bond 0.04251 ( 627) hydrogen bonds : angle 4.02766 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 378 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8753 (m110) cc_final: 0.8142 (t0) REVERT: B 398 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: B 446 GLU cc_start: 0.8844 (mp0) cc_final: 0.8258 (mp0) REVERT: C 73 ASP cc_start: 0.8663 (t0) cc_final: 0.8404 (t0) REVERT: D 78 GLN cc_start: 0.8275 (mt0) cc_final: 0.7489 (mp10) REVERT: D 81 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8106 (tp) REVERT: D 111 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8738 (mm-40) REVERT: E 11 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: F 78 GLN cc_start: 0.8071 (pt0) cc_final: 0.7576 (pm20) REVERT: F 82 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7535 (tm-30) REVERT: G 17 ASP cc_start: 0.8076 (m-30) cc_final: 0.7744 (m-30) REVERT: Y 73 ASP cc_start: 0.8751 (t0) cc_final: 0.8437 (t0) outliers start: 64 outliers final: 53 residues processed: 406 average time/residue: 0.1291 time to fit residues: 76.5245 Evaluate side-chains 434 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 176 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 144 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108283 restraints weight = 20006.876| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.73 r_work: 0.3174 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14709 Z= 0.117 Angle : 0.578 10.896 19938 Z= 0.291 Chirality : 0.040 0.250 2248 Planarity : 0.004 0.050 2508 Dihedral : 3.775 19.873 2000 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.12 % Allowed : 24.05 % Favored : 72.84 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1824 helix: 2.11 (0.21), residues: 636 sheet: -0.38 (0.27), residues: 372 loop : -2.07 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 101 TYR 0.017 0.001 TYR B 463 PHE 0.015 0.001 PHE A 293 TRP 0.013 0.001 TRP F 35 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00276 (14698) covalent geometry : angle 0.57787 (19916) SS BOND : bond 0.00266 ( 11) SS BOND : angle 0.99395 ( 22) hydrogen bonds : bond 0.03372 ( 627) hydrogen bonds : angle 3.88595 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8504 (m110) cc_final: 0.7752 (t0) REVERT: B 351 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8305 (tp-100) REVERT: B 398 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: B 446 GLU cc_start: 0.8667 (mp0) cc_final: 0.8093 (mp0) REVERT: C 73 ASP cc_start: 0.8636 (t0) cc_final: 0.8379 (t0) REVERT: D 13 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7184 (ptmm) REVERT: D 78 GLN cc_start: 0.8200 (mt0) cc_final: 0.7473 (mp10) REVERT: E 11 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: E 49 SER cc_start: 0.9257 (t) cc_final: 0.9053 (p) REVERT: F 13 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7396 (ptmm) REVERT: F 78 GLN cc_start: 0.7957 (pt0) cc_final: 0.7530 (pm20) REVERT: F 82 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7497 (tm-30) REVERT: G 17 ASP cc_start: 0.7959 (m-30) cc_final: 0.7687 (m-30) REVERT: Y 73 ASP cc_start: 0.8762 (t0) cc_final: 0.8375 (t0) outliers start: 49 outliers final: 45 residues processed: 417 average time/residue: 0.1280 time to fit residues: 78.0322 Evaluate side-chains 429 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 382 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107074 restraints weight = 19932.596| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.71 r_work: 0.3160 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14709 Z= 0.136 Angle : 0.593 11.352 19938 Z= 0.300 Chirality : 0.041 0.248 2248 Planarity : 0.004 0.051 2508 Dihedral : 3.770 19.990 2000 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.63 % Allowed : 23.98 % Favored : 72.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1824 helix: 2.15 (0.21), residues: 636 sheet: -0.41 (0.26), residues: 392 loop : -2.03 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 101 TYR 0.016 0.001 TYR B 336 PHE 0.015 0.001 PHE A 293 TRP 0.009 0.001 TRP D 35 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00326 (14698) covalent geometry : angle 0.59234 (19916) SS BOND : bond 0.00321 ( 11) SS BOND : angle 1.06556 ( 22) hydrogen bonds : bond 0.03570 ( 627) hydrogen bonds : angle 3.90864 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4473.38 seconds wall clock time: 77 minutes 15.47 seconds (4635.47 seconds total)