Starting phenix.real_space_refine on Sat Sep 12 00:52:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.map" model { file = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6eti_3953/09_2026/6eti_3953.cif" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8036 2.51 5 N 2042 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12442 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.21 Number of scatterers: 12442 At special positions: 0 Unit cell: (103.32, 99.96, 146.16, 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 68 16.00 O 2296 8.00 N 2042 7.00 C 8036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 445.7 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 44.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.794A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.546A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.572A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.773A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.724A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.598A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.860A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.743A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.507A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.518A pdb=" N LEU A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 396 through 413 Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.525A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 removed outlier: 3.847A pdb=" N ALA A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.835A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 451' Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.659A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 3.629A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.791A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 3.584A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.507A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 removed outlier: 4.191A pdb=" N GLY A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.776A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.826A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.661A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.795A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.547A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.573A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.774A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.724A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.598A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.860A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.743A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.508A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.518A pdb=" N LEU B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 396 through 413 Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.526A pdb=" N GLN B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 removed outlier: 3.848A pdb=" N ALA B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.835A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 451' Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.659A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.629A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 3.792A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.583A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 removed outlier: 3.507A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 553 removed outlier: 4.191A pdb=" N GLY B 553 " --> pdb=" O ILE B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 553' Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.775A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.826A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.661A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.856A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.855A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.439A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.438A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.351A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.312A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.312A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.352A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.312A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.312A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1572 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: 2.13 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1946 1.31 - 1.43: 3574 1.43 - 1.56: 7098 1.56 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 12724 Sorted by residual: bond pdb=" C36 BWQ B1101 " pdb=" O37 BWQ B1101 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C36 BWQ A1101 " pdb=" O37 BWQ A1101 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C23 BWQ A1101 " pdb=" O24 BWQ A1101 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C23 BWQ B1101 " pdb=" O24 BWQ B1101 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C23 BWQ A1101 " pdb=" N25 BWQ A1101 " ideal model delta sigma weight residual 1.333 1.466 -0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 12719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 16951 3.36 - 6.72: 241 6.72 - 10.09: 54 10.09 - 13.45: 4 13.45 - 16.81: 4 Bond angle restraints: 17254 Sorted by residual: angle pdb=" C06 BWQ A1101 " pdb=" N07 BWQ A1101 " pdb=" C08 BWQ A1101 " ideal model delta sigma weight residual 109.00 123.58 -14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CA LEU B 64 " pdb=" CB LEU B 64 " pdb=" CG LEU B 64 " ideal model delta sigma weight residual 116.30 133.11 -16.81 3.50e+00 8.16e-02 2.31e+01 angle pdb=" C ILE A 63 " pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 angle pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sigma weight residual 116.30 133.05 -16.75 3.50e+00 8.16e-02 2.29e+01 angle pdb=" C ILE B 63 " pdb=" N LEU B 64 " pdb=" CA LEU B 64 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 ... (remaining 17249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 6971 14.70 - 29.40: 343 29.40 - 44.09: 83 44.09 - 58.79: 15 58.79 - 73.49: 11 Dihedral angle restraints: 7423 sinusoidal: 2887 harmonic: 4536 Sorted by residual: dihedral pdb=" CA PHE A 414 " pdb=" C PHE A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta harmonic sigma weight residual -180.00 -137.37 -42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE B 414 " pdb=" C PHE B 414 " pdb=" N GLY B 415 " pdb=" CA GLY B 415 " ideal model delta harmonic sigma weight residual 180.00 -137.44 -42.56 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 29.37 63.63 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 7420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1393 0.057 - 0.113: 460 0.113 - 0.170: 83 0.170 - 0.226: 32 0.226 - 0.283: 4 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C22 BWQ A1101 " pdb=" C21 BWQ A1101 " pdb=" C23 BWQ A1101 " pdb=" N38 BWQ A1101 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C22 BWQ B1101 " pdb=" C21 BWQ B1101 " pdb=" C23 BWQ B1101 " pdb=" N38 BWQ B1101 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1969 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 BWQ B1101 " 0.030 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C23 BWQ B1101 " 0.065 2.00e-02 2.50e+03 pdb=" C26 BWQ B1101 " -0.266 2.00e-02 2.50e+03 pdb=" N25 BWQ B1101 " 0.354 2.00e-02 2.50e+03 pdb=" O24 BWQ B1101 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ B1101 " -0.169 2.00e-02 2.50e+03 1.92e-01 5.54e+02 pdb=" C22 BWQ B1101 " 0.266 2.00e-02 2.50e+03 pdb=" C26 BWQ B1101 " -0.175 2.00e-02 2.50e+03 pdb=" C36 BWQ B1101 " -0.022 2.00e-02 2.50e+03 pdb=" N38 BWQ B1101 " -0.158 2.00e-02 2.50e+03 pdb=" O37 BWQ B1101 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ A1101 " 0.010 2.00e-02 2.50e+03 8.66e-02 1.12e+02 pdb=" C22 BWQ A1101 " -0.120 2.00e-02 2.50e+03 pdb=" C26 BWQ A1101 " 0.036 2.00e-02 2.50e+03 pdb=" C36 BWQ A1101 " 0.029 2.00e-02 2.50e+03 pdb=" N38 BWQ A1101 " 0.140 2.00e-02 2.50e+03 pdb=" O37 BWQ A1101 " -0.094 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4024 2.83 - 3.35: 10514 3.35 - 3.87: 19620 3.87 - 4.38: 23658 4.38 - 4.90: 41374 Nonbonded interactions: 99190 Sorted by model distance: nonbonded pdb=" OG SER C 63 " pdb=" OG SER C 74 " model vdw 2.316 3.040 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 74 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.362 3.040 nonbonded pdb=" O GLY D 66 " pdb=" NH1 ARG D 84 " model vdw 2.366 3.120 ... (remaining 99185 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 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 : 0.010 0.173 12735 Z= 0.450 Angle : 1.101 16.810 17280 Z= 0.545 Chirality : 0.060 0.283 1972 Planarity : 0.010 0.217 2144 Dihedral : 10.205 73.491 4506 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.33 % Favored : 94.48 % Rotamer: Outliers : 0.30 % Allowed : 3.56 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.70 (0.16), residues: 1558 helix: -4.25 (0.08), residues: 648 sheet: -1.42 (0.30), residues: 272 loop : -2.39 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 426 TYR 0.042 0.004 TYR A 570 PHE 0.048 0.004 PHE E 98 TRP 0.030 0.004 TRP E 96 HIS 0.011 0.003 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.45 (12724) covalent geometry : angle 1.09036 / 0.54 (17254) SS BOND : bond 0.00853 / 0.54 ( 7) SS BOND : angle 2.70584 / 1.80 ( 14) hydrogen bonds : bond 0.30306 / 19.60 ( 534) hydrogen bonds : angle 9.70086 / 6.67 ( 1572) link_BETA1-4 : bond 0.01934 / 0.97 ( 2) link_BETA1-4 : angle 4.69425 / 2.93 ( 6) link_NAG-ASN : bond 0.00834 / 0.44 ( 2) link_NAG-ASN : angle 5.81929 / 3.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8303 (t70) cc_final: 0.8096 (t-90) REVERT: A 475 LEU cc_start: 0.8865 (tp) cc_final: 0.8562 (mp) REVERT: B 243 HIS cc_start: 0.8289 (t70) cc_final: 0.7846 (t-90) REVERT: B 348 GLU cc_start: 0.8158 (tp30) cc_final: 0.7630 (mt-10) outliers start: 4 outliers final: 0 residues processed: 226 average time/residue: 0.1389 time to fit residues: 43.4463 Evaluate side-chains 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN A 68 ASN A 76 ASN A 116 ASN A 243 HIS A 375 HIS A 425 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN B 76 ASN B 120 ASN B 243 HIS B 375 HIS B 425 ASN B 437 GLN B 583 HIS B 601 ASN F 3 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109711 restraints weight = 16337.076| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.59 r_work: 0.3008 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12735 Z= 0.142 Angle : 0.661 8.725 17280 Z= 0.338 Chirality : 0.043 0.179 1972 Planarity : 0.005 0.043 2144 Dihedral : 5.728 68.461 1718 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 6.74 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.46 (0.19), residues: 1558 helix: -1.63 (0.17), residues: 666 sheet: -0.71 (0.31), residues: 272 loop : -1.88 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 575 TYR 0.016 0.002 TYR A 570 PHE 0.042 0.002 PHE A 293 TRP 0.014 0.002 TRP D 109 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12724) covalent geometry : angle 0.65837 / 0.34 (17254) SS BOND : bond 0.00527 / 0.31 ( 7) SS BOND : angle 1.18991 / 0.79 ( 14) hydrogen bonds : bond 0.04898 / 3.17 ( 534) hydrogen bonds : angle 4.77643 / 3.28 ( 1572) link_BETA1-4 : bond 0.00613 / 0.30 ( 2) link_BETA1-4 : angle 1.80074 / 1.07 ( 6) link_NAG-ASN : bond 0.00234 / 0.12 ( 2) link_NAG-ASN : angle 2.36784 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7768 (p0) cc_final: 0.7232 (p0) REVERT: A 203 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7749 (t70) REVERT: A 271 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7724 (mp10) REVERT: B 226 LEU cc_start: 0.8782 (mt) cc_final: 0.8580 (mt) REVERT: B 243 HIS cc_start: 0.8597 (t-90) cc_final: 0.8381 (t70) REVERT: B 335 ILE cc_start: 0.8466 (mt) cc_final: 0.8265 (mp) REVERT: B 348 GLU cc_start: 0.8433 (tp30) cc_final: 0.8078 (tt0) REVERT: B 565 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 600 ASN cc_start: 0.6349 (t0) cc_final: 0.6121 (t0) outliers start: 17 outliers final: 8 residues processed: 178 average time/residue: 0.1225 time to fit residues: 31.2051 Evaluate side-chains 153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103261 restraints weight = 16789.161| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.85 r_work: 0.2833 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12735 Z= 0.283 Angle : 0.741 10.258 17280 Z= 0.370 Chirality : 0.048 0.203 1972 Planarity : 0.005 0.047 2144 Dihedral : 5.925 71.738 1718 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 8.37 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.53 (0.20), residues: 1558 helix: -0.46 (0.19), residues: 670 sheet: -0.48 (0.32), residues: 278 loop : -1.79 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 32 TYR 0.026 0.003 TYR A 570 PHE 0.033 0.002 PHE B 293 TRP 0.012 0.003 TRP F 109 HIS 0.007 0.002 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.28 (12724) covalent geometry : angle 0.73746 / 0.37 (17254) SS BOND : bond 0.00779 / 0.50 ( 7) SS BOND : angle 1.97278 / 1.38 ( 14) hydrogen bonds : bond 0.05421 / 3.51 ( 534) hydrogen bonds : angle 4.60995 / 3.18 ( 1572) link_BETA1-4 : bond 0.01117 / 0.57 ( 2) link_BETA1-4 : angle 1.69955 / 1.05 ( 6) link_NAG-ASN : bond 0.00206 / 0.11 ( 2) link_NAG-ASN : angle 2.49542 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.486 Fit side-chains REVERT: A 127 ASP cc_start: 0.7795 (p0) cc_final: 0.7339 (p0) REVERT: A 203 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7659 (t70) REVERT: A 220 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7254 (t) REVERT: A 271 GLN cc_start: 0.8416 (mm-40) cc_final: 0.7655 (mp10) REVERT: B 226 LEU cc_start: 0.8773 (mt) cc_final: 0.8562 (mt) REVERT: B 348 GLU cc_start: 0.8333 (tp30) cc_final: 0.8070 (tt0) outliers start: 28 outliers final: 23 residues processed: 162 average time/residue: 0.1163 time to fit residues: 27.5435 Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105312 restraints weight = 16341.281| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.60 r_work: 0.2968 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12735 Z= 0.131 Angle : 0.598 7.972 17280 Z= 0.303 Chirality : 0.042 0.139 1972 Planarity : 0.004 0.039 2144 Dihedral : 5.582 79.587 1718 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.63 % Allowed : 9.48 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1558 helix: 0.45 (0.21), residues: 662 sheet: -0.41 (0.32), residues: 278 loop : -1.64 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.017 0.001 TYR A 342 PHE 0.033 0.002 PHE B 293 TRP 0.011 0.001 TRP B 379 HIS 0.008 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12724) covalent geometry : angle 0.59520 / 0.30 (17254) SS BOND : bond 0.00459 / 0.27 ( 7) SS BOND : angle 1.19218 / 0.79 ( 14) hydrogen bonds : bond 0.03929 / 2.54 ( 534) hydrogen bonds : angle 4.16937 / 2.87 ( 1572) link_BETA1-4 : bond 0.00876 / 0.44 ( 2) link_BETA1-4 : angle 1.68488 / 1.00 ( 6) link_NAG-ASN : bond 0.00176 / 0.09 ( 2) link_NAG-ASN : angle 2.05118 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.452 Fit side-chains REVERT: A 127 ASP cc_start: 0.7651 (p0) cc_final: 0.7219 (p0) REVERT: A 203 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7645 (t70) REVERT: A 220 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7087 (t) REVERT: A 271 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7653 (mp10) REVERT: B 348 GLU cc_start: 0.8369 (tp30) cc_final: 0.8107 (tt0) REVERT: B 502 LYS cc_start: 0.8236 (mmtt) cc_final: 0.8018 (mptt) outliers start: 22 outliers final: 14 residues processed: 156 average time/residue: 0.1083 time to fit residues: 25.0894 Evaluate side-chains 142 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102877 restraints weight = 16579.671| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.79 r_work: 0.2874 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12735 Z= 0.222 Angle : 0.678 7.924 17280 Z= 0.338 Chirality : 0.046 0.215 1972 Planarity : 0.004 0.040 2144 Dihedral : 5.753 80.874 1718 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.37 % Allowed : 9.41 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.63 (0.21), residues: 1558 helix: 0.63 (0.21), residues: 662 sheet: -0.27 (0.33), residues: 274 loop : -1.61 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.017 0.002 TYR B 570 PHE 0.032 0.002 PHE B 293 TRP 0.009 0.002 TRP C 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.22 (12724) covalent geometry : angle 0.67440 / 0.34 (17254) SS BOND : bond 0.00709 / 0.45 ( 7) SS BOND : angle 1.77614 / 1.22 ( 14) hydrogen bonds : bond 0.04493 / 2.89 ( 534) hydrogen bonds : angle 4.25762 / 2.94 ( 1572) link_BETA1-4 : bond 0.00969 / 0.48 ( 2) link_BETA1-4 : angle 1.63217 / 1.00 ( 6) link_NAG-ASN : bond 0.00285 / 0.15 ( 2) link_NAG-ASN : angle 2.28042 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.514 Fit side-chains REVERT: A 127 ASP cc_start: 0.7666 (p0) cc_final: 0.6952 (p0) REVERT: A 203 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7615 (t70) REVERT: A 271 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7656 (mp10) REVERT: B 127 ASP cc_start: 0.7910 (p0) cc_final: 0.7342 (p0) REVERT: B 348 GLU cc_start: 0.8293 (tp30) cc_final: 0.8089 (tt0) REVERT: B 614 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9283 (mp) REVERT: D 47 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8283 (tt0) outliers start: 32 outliers final: 23 residues processed: 161 average time/residue: 0.1101 time to fit residues: 26.2023 Evaluate side-chains 150 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105486 restraints weight = 16390.072| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.60 r_work: 0.2950 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12735 Z= 0.118 Angle : 0.585 7.664 17280 Z= 0.295 Chirality : 0.042 0.203 1972 Planarity : 0.003 0.041 2144 Dihedral : 5.534 84.346 1718 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.37 % Allowed : 9.48 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1558 helix: 1.02 (0.21), residues: 666 sheet: -0.25 (0.32), residues: 276 loop : -1.48 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.016 0.001 TYR A 342 PHE 0.033 0.002 PHE B 293 TRP 0.010 0.001 TRP A 379 HIS 0.009 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12724) covalent geometry : angle 0.58257 / 0.29 (17254) SS BOND : bond 0.00441 / 0.26 ( 7) SS BOND : angle 1.11820 / 0.74 ( 14) hydrogen bonds : bond 0.03610 / 2.33 ( 534) hydrogen bonds : angle 4.03139 / 2.78 ( 1572) link_BETA1-4 : bond 0.00596 / 0.30 ( 2) link_BETA1-4 : angle 1.69825 / 1.02 ( 6) link_NAG-ASN : bond 0.00204 / 0.10 ( 2) link_NAG-ASN : angle 1.96683 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.480 Fit side-chains REVERT: A 127 ASP cc_start: 0.7687 (p0) cc_final: 0.7232 (p0) REVERT: A 271 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8252 (pt0) REVERT: B 127 ASP cc_start: 0.8014 (p0) cc_final: 0.7173 (p0) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.1097 time to fit residues: 26.0233 Evaluate side-chains 143 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105160 restraints weight = 16439.011| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.64 r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12735 Z= 0.153 Angle : 0.617 11.033 17280 Z= 0.309 Chirality : 0.044 0.305 1972 Planarity : 0.004 0.042 2144 Dihedral : 5.587 85.876 1718 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.93 % Allowed : 9.85 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1558 helix: 1.16 (0.21), residues: 666 sheet: -0.23 (0.32), residues: 278 loop : -1.39 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.018 0.002 TYR A 342 PHE 0.033 0.002 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.009 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (12724) covalent geometry : angle 0.61457 / 0.31 (17254) SS BOND : bond 0.00543 / 0.33 ( 7) SS BOND : angle 1.40819 / 0.95 ( 14) hydrogen bonds : bond 0.03811 / 2.45 ( 534) hydrogen bonds : angle 4.04354 / 2.80 ( 1572) link_BETA1-4 : bond 0.00824 / 0.41 ( 2) link_BETA1-4 : angle 1.61141 / 0.96 ( 6) link_NAG-ASN : bond 0.00257 / 0.13 ( 2) link_NAG-ASN : angle 1.98547 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.524 Fit side-chains REVERT: A 127 ASP cc_start: 0.7640 (p0) cc_final: 0.7212 (p0) REVERT: A 271 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8251 (pt0) REVERT: B 127 ASP cc_start: 0.7974 (p0) cc_final: 0.7517 (p0) REVERT: D 47 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8418 (tt0) outliers start: 26 outliers final: 25 residues processed: 150 average time/residue: 0.1128 time to fit residues: 24.8946 Evaluate side-chains 149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 0.0170 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106712 restraints weight = 16355.141| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.66 r_work: 0.2960 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12735 Z= 0.114 Angle : 0.583 11.345 17280 Z= 0.295 Chirality : 0.042 0.312 1972 Planarity : 0.003 0.041 2144 Dihedral : 5.486 87.345 1718 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.78 % Allowed : 10.44 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.22), residues: 1558 helix: 1.43 (0.21), residues: 666 sheet: -0.21 (0.32), residues: 278 loop : -1.31 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.018 0.001 TYR A 342 PHE 0.034 0.001 PHE A 293 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (12724) covalent geometry : angle 0.58075 / 0.29 (17254) SS BOND : bond 0.00397 / 0.22 ( 7) SS BOND : angle 1.09864 / 0.74 ( 14) hydrogen bonds : bond 0.03448 / 2.23 ( 534) hydrogen bonds : angle 3.94672 / 2.73 ( 1572) link_BETA1-4 : bond 0.00726 / 0.37 ( 2) link_BETA1-4 : angle 1.65164 / 0.97 ( 6) link_NAG-ASN : bond 0.00227 / 0.11 ( 2) link_NAG-ASN : angle 1.81344 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.502 Fit side-chains REVERT: A 127 ASP cc_start: 0.7554 (p0) cc_final: 0.7235 (p0) REVERT: A 162 ASN cc_start: 0.8945 (m-40) cc_final: 0.8597 (m-40) REVERT: A 271 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8250 (pt0) REVERT: B 127 ASP cc_start: 0.7788 (p0) cc_final: 0.7265 (p0) REVERT: B 271 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8330 (pt0) REVERT: F 47 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8386 (tt0) outliers start: 24 outliers final: 21 residues processed: 154 average time/residue: 0.1089 time to fit residues: 24.7116 Evaluate side-chains 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 243 HIS B 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105576 restraints weight = 16335.647| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.62 r_work: 0.2920 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12735 Z= 0.169 Angle : 0.635 11.812 17280 Z= 0.316 Chirality : 0.045 0.310 1972 Planarity : 0.004 0.038 2144 Dihedral : 5.612 86.876 1718 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 10.00 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1558 helix: 1.36 (0.21), residues: 666 sheet: -0.15 (0.32), residues: 278 loop : -1.28 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 65 TYR 0.017 0.002 TYR A 342 PHE 0.038 0.002 PHE B 293 TRP 0.009 0.002 TRP B 379 HIS 0.008 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (12724) covalent geometry : angle 0.63183 / 0.32 (17254) SS BOND : bond 0.00665 / 0.44 ( 7) SS BOND : angle 1.53666 / 1.05 ( 14) hydrogen bonds : bond 0.03866 / 2.48 ( 534) hydrogen bonds : angle 4.04400 / 2.80 ( 1572) link_BETA1-4 : bond 0.00886 / 0.44 ( 2) link_BETA1-4 : angle 1.59314 / 0.95 ( 6) link_NAG-ASN : bond 0.00328 / 0.16 ( 2) link_NAG-ASN : angle 1.89500 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.402 Fit side-chains REVERT: A 127 ASP cc_start: 0.7573 (p0) cc_final: 0.7142 (p0) REVERT: A 271 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8253 (pt0) REVERT: A 349 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6505 (mp) REVERT: B 127 ASP cc_start: 0.7841 (p0) cc_final: 0.7321 (p0) REVERT: B 271 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8358 (pt0) REVERT: D 47 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: F 47 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8439 (tt0) outliers start: 28 outliers final: 25 residues processed: 150 average time/residue: 0.1101 time to fit residues: 24.6902 Evaluate side-chains 149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105808 restraints weight = 16479.296| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.65 r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12735 Z= 0.117 Angle : 0.601 11.560 17280 Z= 0.303 Chirality : 0.043 0.295 1972 Planarity : 0.003 0.037 2144 Dihedral : 5.488 88.458 1718 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.00 % Allowed : 10.22 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1558 helix: 1.51 (0.21), residues: 666 sheet: -0.14 (0.32), residues: 282 loop : -1.19 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.018 0.001 TYR A 342 PHE 0.034 0.002 PHE A 293 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12724) covalent geometry : angle 0.59897 / 0.30 (17254) SS BOND : bond 0.00394 / 0.22 ( 7) SS BOND : angle 1.25148 / 0.87 ( 14) hydrogen bonds : bond 0.03485 / 2.26 ( 534) hydrogen bonds : angle 3.95977 / 2.74 ( 1572) link_BETA1-4 : bond 0.00765 / 0.38 ( 2) link_BETA1-4 : angle 1.63683 / 0.96 ( 6) link_NAG-ASN : bond 0.00244 / 0.12 ( 2) link_NAG-ASN : angle 1.79380 / 1.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.505 Fit side-chains REVERT: A 127 ASP cc_start: 0.7497 (p0) cc_final: 0.7074 (p0) REVERT: A 271 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8235 (pt0) REVERT: A 349 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6327 (mp) REVERT: B 127 ASP cc_start: 0.7779 (p0) cc_final: 0.7271 (p0) REVERT: B 271 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8302 (pt0) REVERT: D 47 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: F 47 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8371 (tt0) outliers start: 27 outliers final: 23 residues processed: 156 average time/residue: 0.1089 time to fit residues: 25.4481 Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106494 restraints weight = 16369.344| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.63 r_work: 0.2952 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12735 Z= 0.125 Angle : 0.608 11.278 17280 Z= 0.304 Chirality : 0.043 0.276 1972 Planarity : 0.003 0.044 2144 Dihedral : 5.484 89.030 1718 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.93 % Allowed : 10.30 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1558 helix: 1.54 (0.21), residues: 666 sheet: -0.09 (0.32), residues: 278 loop : -1.16 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.017 0.001 TYR A 342 PHE 0.039 0.002 PHE B 293 TRP 0.010 0.001 TRP A 379 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (12724) covalent geometry : angle 0.60552 / 0.30 (17254) SS BOND : bond 0.00474 / 0.29 ( 7) SS BOND : angle 1.48097 / 1.01 ( 14) hydrogen bonds : bond 0.03470 / 2.24 ( 534) hydrogen bonds : angle 3.96937 / 2.75 ( 1572) link_BETA1-4 : bond 0.00850 / 0.42 ( 2) link_BETA1-4 : angle 1.58433 / 0.92 ( 6) link_NAG-ASN : bond 0.00275 / 0.14 ( 2) link_NAG-ASN : angle 1.78518 / 1.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.62 seconds wall clock time: 53 minutes 46.61 seconds (3226.61 seconds total)