Starting phenix.real_space_refine on Wed Mar 4 22:20:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl6_25192/03_2026/7sl6_25192.map" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. 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 112 5.16 5 C 8892 2.51 5 N 2406 2.21 5 O 2594 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 217 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "F" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 217 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 3.29, per 1000 atoms: 0.23 Number of scatterers: 14004 At special positions: 0 Unit cell: (147.96, 100.44, 173.88, 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 112 16.00 O 2594 8.00 N 2406 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " 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: 1.21 Conformation dependent library (CDL) restraints added in 526.8 milliseconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 33 sheets defined 18.5% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.788A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.954A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.653A pdb=" N ARG A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.915A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.805A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.735A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.631A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 378 through 382 removed outlier: 4.480A pdb=" N PHE A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 382 " --> pdb=" O LEU A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 382' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.592A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.654A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.597A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 716 removed outlier: 3.500A pdb=" N ILE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 695 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.960A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.922A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.644A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.930A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.797A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.737A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.647A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.490A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.602A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.621A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.673A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 3.751A pdb=" N LEU B 695 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.714A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 14 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.964A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 145 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU A 120 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 147 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.603A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.507A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.160A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.692A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 567 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 508 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 6.274A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB7, first strand: chain 'A' and resid 858 through 864 removed outlier: 3.838A pdb=" N LEU A 846 " --> pdb=" O THR A 891 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.977A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 145 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU B 120 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 147 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.566A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.463A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.626A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC5, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.510A pdb=" N ASN B 337 " --> pdb=" O CYS B 312 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 319 through 321 removed outlier: 7.130A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.517A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 567 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.704A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.679A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 858 through 864 removed outlier: 3.891A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 873 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: 2.57 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4587 1.34 - 1.46: 3346 1.46 - 1.58: 6277 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14346 Sorted by residual: bond pdb=" CA TYR B 581 " pdb=" CB TYR B 581 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.69e-02 3.50e+03 1.75e+00 bond pdb=" CG GLU A 697 " pdb=" CD GLU A 697 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" CG GLU E 13 " pdb=" CD GLU E 13 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" C SER A 792 " pdb=" N PRO A 793 " ideal model delta sigma weight residual 1.340 1.369 -0.029 2.76e-02 1.31e+03 1.10e+00 ... (remaining 14341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 19253 2.33 - 4.66: 172 4.66 - 6.98: 13 6.98 - 9.31: 4 9.31 - 11.64: 2 Bond angle restraints: 19444 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA TYR B 581 " pdb=" CB TYR B 581 " pdb=" CG TYR B 581 " ideal model delta sigma weight residual 113.90 122.94 -9.04 1.80e+00 3.09e-01 2.52e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" N TYR A 581 " pdb=" CA TYR A 581 " pdb=" CB TYR A 581 " ideal model delta sigma weight residual 110.49 118.58 -8.09 1.69e+00 3.50e-01 2.29e+01 angle pdb=" N GLU A 697 " pdb=" CA GLU A 697 " pdb=" CB GLU A 697 " ideal model delta sigma weight residual 110.28 115.75 -5.47 1.55e+00 4.16e-01 1.25e+01 ... (remaining 19439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 7844 17.36 - 34.72: 695 34.72 - 52.07: 124 52.07 - 69.43: 27 69.43 - 86.79: 14 Dihedral angle restraints: 8704 sinusoidal: 3638 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -150.13 64.13 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.73 61.73 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.10 -56.10 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1383 0.034 - 0.068: 471 0.068 - 0.102: 161 0.102 - 0.136: 83 0.136 - 0.169: 10 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CB VAL B 572 " pdb=" CA VAL B 572 " pdb=" CG1 VAL B 572 " pdb=" CG2 VAL B 572 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2105 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C THR B 580 " 0.052 2.00e-02 2.50e+03 pdb=" O THR B 580 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 581 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 581 " 0.007 2.00e-02 2.50e+03 1.65e-02 5.43e+00 pdb=" CG TYR A 581 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 581 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 581 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 581 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 581 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 836 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 837 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 837 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 837 " -0.018 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1069 2.74 - 3.28: 13867 3.28 - 3.82: 22763 3.82 - 4.36: 26995 4.36 - 4.90: 46368 Nonbonded interactions: 111062 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 12 " pdb=" OE1 GLN C 15 " model vdw 2.202 3.040 nonbonded pdb=" O ARG A 776 " pdb=" OG1 THR A 779 " model vdw 2.241 3.040 nonbonded pdb=" O GLU A 826 " pdb=" OH TYR A 910 " model vdw 2.255 3.040 nonbonded pdb=" O GLU B 826 " pdb=" OH TYR B 910 " model vdw 2.270 3.040 ... (remaining 111057 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 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.890 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14386 Z= 0.123 Angle : 0.553 11.641 19524 Z= 0.292 Chirality : 0.043 0.169 2108 Planarity : 0.003 0.032 2514 Dihedral : 13.379 86.791 5312 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.29 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1698 helix: 0.30 (0.37), residues: 206 sheet: 0.56 (0.32), residues: 316 loop : -0.92 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 86 TYR 0.038 0.001 TYR A 581 PHE 0.009 0.001 PHE A 381 TRP 0.009 0.001 TRP B 414 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00274 (14346) covalent geometry : angle 0.55210 (19444) SS BOND : bond 0.00178 ( 40) SS BOND : angle 0.81755 ( 80) hydrogen bonds : bond 0.23115 ( 346) hydrogen bonds : angle 8.11359 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 0.1142 time to fit residues: 10.2894 Evaluate side-chains 39 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 90 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 612 GLN A 867 HIS B 34 GLN B 90 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 612 GLN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.062856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044636 restraints weight = 73788.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045683 restraints weight = 43113.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046380 restraints weight = 31104.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046809 restraints weight = 25369.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047104 restraints weight = 22368.467| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 14386 Z= 0.333 Angle : 0.709 7.433 19524 Z= 0.372 Chirality : 0.048 0.183 2108 Planarity : 0.005 0.038 2514 Dihedral : 5.118 17.823 1894 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.70 % Allowed : 8.10 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.21), residues: 1698 helix: -0.31 (0.35), residues: 236 sheet: 0.35 (0.29), residues: 340 loop : -1.19 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 86 TYR 0.022 0.002 TYR B 847 PHE 0.022 0.002 PHE A 381 TRP 0.015 0.002 TRP A 183 HIS 0.007 0.002 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00770 (14346) covalent geometry : angle 0.70808 (19444) SS BOND : bond 0.00406 ( 40) SS BOND : angle 0.99061 ( 80) hydrogen bonds : bond 0.05062 ( 346) hydrogen bonds : angle 6.48946 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.457 Fit side-chains REVERT: B 651 LYS cc_start: 0.8438 (mttt) cc_final: 0.7914 (ptmm) REVERT: B 834 TRP cc_start: 0.3200 (p90) cc_final: 0.2617 (p90) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.1075 time to fit residues: 9.8193 Evaluate side-chains 45 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.063966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.045834 restraints weight = 72805.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046913 restraints weight = 42029.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047623 restraints weight = 30116.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048075 restraints weight = 24426.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048374 restraints weight = 21428.311| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14386 Z= 0.136 Angle : 0.552 8.447 19524 Z= 0.288 Chirality : 0.044 0.174 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.722 19.234 1894 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.38 % Allowed : 9.94 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1698 helix: 0.25 (0.37), residues: 224 sheet: 0.29 (0.29), residues: 348 loop : -0.98 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.027 0.001 TYR A 847 PHE 0.013 0.001 PHE B 567 TRP 0.009 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00315 (14346) covalent geometry : angle 0.55126 (19444) SS BOND : bond 0.00206 ( 40) SS BOND : angle 0.66114 ( 80) hydrogen bonds : bond 0.04255 ( 346) hydrogen bonds : angle 6.04429 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.393 Fit side-chains REVERT: A 300 MET cc_start: 0.7517 (tmm) cc_final: 0.7260 (tmm) REVERT: A 581 TYR cc_start: 0.5650 (m-80) cc_final: 0.5345 (m-80) REVERT: B 11 MET cc_start: 0.8509 (pmm) cc_final: 0.8263 (pmm) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0987 time to fit residues: 7.6747 Evaluate side-chains 44 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.062050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044041 restraints weight = 73688.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045070 restraints weight = 43054.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045743 restraints weight = 31042.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.046187 restraints weight = 25279.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046465 restraints weight = 22178.289| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 14386 Z= 0.322 Angle : 0.691 6.820 19524 Z= 0.358 Chirality : 0.047 0.194 2108 Planarity : 0.005 0.038 2514 Dihedral : 5.275 18.080 1894 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.65 % Allowed : 12.22 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1698 helix: -0.48 (0.34), residues: 236 sheet: 0.05 (0.29), residues: 350 loop : -1.24 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 865 TYR 0.021 0.002 TYR A 581 PHE 0.022 0.002 PHE B 381 TRP 0.014 0.002 TRP B 634 HIS 0.008 0.002 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00738 (14346) covalent geometry : angle 0.68976 (19444) SS BOND : bond 0.00332 ( 40) SS BOND : angle 0.95117 ( 80) hydrogen bonds : bond 0.04579 ( 346) hydrogen bonds : angle 6.21759 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 530 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 530 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (p) REVERT: B 634 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7197 (m-90) outliers start: 26 outliers final: 15 residues processed: 68 average time/residue: 0.0844 time to fit residues: 9.6250 Evaluate side-chains 56 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.063301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045268 restraints weight = 73152.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046357 restraints weight = 42463.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047073 restraints weight = 30396.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047540 restraints weight = 24581.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047824 restraints weight = 21492.366| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14386 Z= 0.139 Angle : 0.554 8.962 19524 Z= 0.287 Chirality : 0.044 0.170 2108 Planarity : 0.003 0.036 2514 Dihedral : 4.846 19.907 1894 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 1.27 % Allowed : 13.61 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1698 helix: 0.07 (0.36), residues: 224 sheet: 0.17 (0.29), residues: 342 loop : -1.05 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 782 TYR 0.016 0.001 TYR B 581 PHE 0.012 0.001 PHE A 567 TRP 0.010 0.001 TRP B 634 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00325 (14346) covalent geometry : angle 0.55369 (19444) SS BOND : bond 0.00201 ( 40) SS BOND : angle 0.64448 ( 80) hydrogen bonds : bond 0.03864 ( 346) hydrogen bonds : angle 5.82250 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.435 Fit side-chains REVERT: A 300 MET cc_start: 0.7453 (tmm) cc_final: 0.7073 (tmm) REVERT: A 634 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6954 (m-90) REVERT: B 634 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.7185 (m-90) outliers start: 20 outliers final: 10 residues processed: 58 average time/residue: 0.0804 time to fit residues: 8.1904 Evaluate side-chains 49 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 0.0770 chunk 153 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.063595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045628 restraints weight = 72715.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046730 restraints weight = 42034.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047445 restraints weight = 29931.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047908 restraints weight = 24199.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048127 restraints weight = 21183.519| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14386 Z= 0.120 Angle : 0.537 10.430 19524 Z= 0.278 Chirality : 0.043 0.169 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.645 18.840 1894 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 1.27 % Allowed : 14.18 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1698 helix: 0.14 (0.36), residues: 224 sheet: 0.16 (0.29), residues: 364 loop : -0.99 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.034 0.001 TYR A 581 PHE 0.012 0.001 PHE B 567 TRP 0.009 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00280 (14346) covalent geometry : angle 0.53638 (19444) SS BOND : bond 0.00190 ( 40) SS BOND : angle 0.57140 ( 80) hydrogen bonds : bond 0.03568 ( 346) hydrogen bonds : angle 5.58664 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 300 MET cc_start: 0.7528 (tmm) cc_final: 0.7297 (tmm) REVERT: A 634 TRP cc_start: 0.7420 (OUTLIER) cc_final: 0.6913 (m-90) REVERT: B 300 MET cc_start: 0.7950 (tpp) cc_final: 0.7681 (tpp) outliers start: 20 outliers final: 15 residues processed: 58 average time/residue: 0.0991 time to fit residues: 9.4307 Evaluate side-chains 53 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045268 restraints weight = 73232.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046346 restraints weight = 42280.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047053 restraints weight = 30188.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047514 restraints weight = 24424.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047796 restraints weight = 21360.917| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14386 Z= 0.165 Angle : 0.556 9.454 19524 Z= 0.286 Chirality : 0.043 0.166 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.686 19.609 1894 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 1.77 % Allowed : 14.24 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1698 helix: 0.13 (0.37), residues: 224 sheet: 0.11 (0.28), residues: 364 loop : -0.96 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 776 TYR 0.016 0.001 TYR B 581 PHE 0.012 0.001 PHE B 381 TRP 0.011 0.001 TRP B 634 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00384 (14346) covalent geometry : angle 0.55561 (19444) SS BOND : bond 0.00206 ( 40) SS BOND : angle 0.67175 ( 80) hydrogen bonds : bond 0.03615 ( 346) hydrogen bonds : angle 5.54501 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 300 MET cc_start: 0.7510 (tmm) cc_final: 0.7270 (tmm) REVERT: A 634 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.6938 (m-90) REVERT: B 558 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 634 TRP cc_start: 0.7661 (OUTLIER) cc_final: 0.7211 (m-90) outliers start: 28 outliers final: 18 residues processed: 65 average time/residue: 0.0823 time to fit residues: 9.2869 Evaluate side-chains 58 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 158 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.062797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044873 restraints weight = 73035.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045936 restraints weight = 42568.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046637 restraints weight = 30468.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047075 restraints weight = 24622.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047360 restraints weight = 21653.121| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14386 Z= 0.201 Angle : 0.588 10.028 19524 Z= 0.302 Chirality : 0.044 0.197 2108 Planarity : 0.004 0.035 2514 Dihedral : 4.827 19.031 1894 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 1.96 % Allowed : 14.49 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1698 helix: 0.04 (0.36), residues: 224 sheet: 0.22 (0.29), residues: 352 loop : -1.04 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 776 TYR 0.023 0.001 TYR B 581 PHE 0.013 0.001 PHE B 381 TRP 0.010 0.001 TRP B 634 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00468 (14346) covalent geometry : angle 0.58760 (19444) SS BOND : bond 0.00218 ( 40) SS BOND : angle 0.75306 ( 80) hydrogen bonds : bond 0.03843 ( 346) hydrogen bonds : angle 5.61825 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 38 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 555 MET cc_start: 0.8404 (mmm) cc_final: 0.8075 (mmm) REVERT: A 558 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8368 (mp) REVERT: A 634 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.6987 (m-90) REVERT: B 300 MET cc_start: 0.8047 (tpp) cc_final: 0.7731 (tpp) REVERT: B 558 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8350 (mm) REVERT: B 634 TRP cc_start: 0.7705 (OUTLIER) cc_final: 0.7257 (m-90) outliers start: 31 outliers final: 21 residues processed: 68 average time/residue: 0.0854 time to fit residues: 10.1319 Evaluate side-chains 62 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 121 optimal weight: 0.4980 chunk 141 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 167 optimal weight: 0.4980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.063210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045322 restraints weight = 73466.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046416 restraints weight = 42410.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047123 restraints weight = 30146.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047580 restraints weight = 24370.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.047875 restraints weight = 21330.224| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14386 Z= 0.149 Angle : 0.573 10.840 19524 Z= 0.290 Chirality : 0.044 0.182 2108 Planarity : 0.003 0.034 2514 Dihedral : 4.719 19.586 1894 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 1.84 % Allowed : 14.81 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.21), residues: 1698 helix: 0.05 (0.36), residues: 226 sheet: 0.18 (0.29), residues: 354 loop : -1.01 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 776 TYR 0.026 0.001 TYR B 581 PHE 0.013 0.001 PHE B 567 TRP 0.009 0.001 TRP B 634 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00350 (14346) covalent geometry : angle 0.57267 (19444) SS BOND : bond 0.00199 ( 40) SS BOND : angle 0.69354 ( 80) hydrogen bonds : bond 0.03654 ( 346) hydrogen bonds : angle 5.52064 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 36 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 634 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.6995 (m-90) REVERT: B 300 MET cc_start: 0.7944 (tpp) cc_final: 0.7689 (tpp) REVERT: B 558 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 634 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.7257 (m-90) outliers start: 29 outliers final: 21 residues processed: 64 average time/residue: 0.0907 time to fit residues: 9.9900 Evaluate side-chains 60 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 overall best weight: 1.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045669 restraints weight = 73126.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046784 restraints weight = 42066.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047509 restraints weight = 29832.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047964 restraints weight = 24001.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048250 restraints weight = 20966.314| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14386 Z= 0.127 Angle : 0.571 18.487 19524 Z= 0.284 Chirality : 0.044 0.361 2108 Planarity : 0.003 0.034 2514 Dihedral : 4.575 19.221 1894 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 1.84 % Allowed : 14.87 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1698 helix: 0.08 (0.36), residues: 226 sheet: 0.39 (0.29), residues: 344 loop : -0.99 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 796 TYR 0.025 0.001 TYR B 581 PHE 0.013 0.001 PHE B 567 TRP 0.008 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00301 (14346) covalent geometry : angle 0.57047 (19444) SS BOND : bond 0.00199 ( 40) SS BOND : angle 0.65462 ( 80) hydrogen bonds : bond 0.03509 ( 346) hydrogen bonds : angle 5.39704 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 634 TRP cc_start: 0.7422 (OUTLIER) cc_final: 0.6943 (m-90) REVERT: B 11 MET cc_start: 0.8429 (pmm) cc_final: 0.8077 (pmm) REVERT: B 300 MET cc_start: 0.7929 (tpp) cc_final: 0.7684 (tpp) REVERT: B 558 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8293 (mm) REVERT: B 634 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.7238 (m-90) outliers start: 29 outliers final: 23 residues processed: 66 average time/residue: 0.0859 time to fit residues: 9.8172 Evaluate side-chains 64 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 127 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046266 restraints weight = 73831.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047394 restraints weight = 42490.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.048126 restraints weight = 30203.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048589 restraints weight = 24350.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048891 restraints weight = 21270.331| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14386 Z= 0.101 Angle : 0.554 15.999 19524 Z= 0.275 Chirality : 0.044 0.379 2108 Planarity : 0.003 0.034 2514 Dihedral : 4.403 19.014 1894 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 1.52 % Allowed : 15.32 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1698 helix: 0.13 (0.36), residues: 226 sheet: 0.28 (0.29), residues: 344 loop : -0.90 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 579 TYR 0.022 0.001 TYR B 581 PHE 0.013 0.001 PHE B 567 TRP 0.011 0.001 TRP B 183 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00240 (14346) covalent geometry : angle 0.55410 (19444) SS BOND : bond 0.00199 ( 40) SS BOND : angle 0.58573 ( 80) hydrogen bonds : bond 0.03298 ( 346) hydrogen bonds : angle 5.26666 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.10 seconds wall clock time: 40 minutes 16.53 seconds (2416.53 seconds total)