Starting phenix.real_space_refine on Tue Nov 18 08:48:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_3953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_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 { model { file = "/net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_3953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_3953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_3953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eti_3953/11_2025/6eti_3953.map" } 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-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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: 3.02, per 1000 atoms: 0.24 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: 0.99 Conformation dependent library (CDL) restraints added in 503.3 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: 0.48 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: 2.11 Time building geometry restraints manager: 1.35 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 - 26.32: 7386 26.32 - 52.63: 165 52.63 - 78.94: 20 78.94 - 105.26: 2 105.26 - 131.57: 6 Dihedral angle restraints: 7579 sinusoidal: 3043 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 7576 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: 3.720 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.390 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 11.802 131.573 4662 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 covalent geometry : bond 0.01046 (12724) covalent geometry : angle 1.09036 (17254) SS BOND : bond 0.00853 ( 7) SS BOND : angle 2.70584 ( 14) hydrogen bonds : bond 0.30306 ( 534) hydrogen bonds : angle 9.70086 ( 1572) link_BETA1-4 : bond 0.01934 ( 2) link_BETA1-4 : angle 4.69425 ( 6) link_NAG-ASN : bond 0.00834 ( 2) link_NAG-ASN : angle 5.81929 ( 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 : 0.509 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: 0.7629 (mt-10) outliers start: 4 outliers final: 0 residues processed: 226 average time/residue: 0.1416 time to fit residues: 43.6800 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 : 0.409 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.137223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109949 restraints weight = 16326.002| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.64 r_work: 0.2997 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 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 0.029 12735 Z= 0.142 Angle : 0.660 8.739 17280 Z= 0.337 Chirality : 0.043 0.219 1972 Planarity : 0.005 0.043 2144 Dihedral : 10.490 132.791 1874 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 6.67 % Favored : 92.07 % 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: -2.48 (0.19), residues: 1558 helix: -1.65 (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 F 84 TYR 0.016 0.002 TYR A 570 PHE 0.040 0.002 PHE A 293 TRP 0.014 0.001 TRP D 109 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00324 (12724) covalent geometry : angle 0.65651 (17254) SS BOND : bond 0.00529 ( 7) SS BOND : angle 1.18915 ( 14) hydrogen bonds : bond 0.04888 ( 534) hydrogen bonds : angle 4.78630 ( 1572) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 2.33336 ( 6) link_NAG-ASN : bond 0.00297 ( 2) link_NAG-ASN : angle 2.20083 ( 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 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7605 (p0) cc_final: 0.7112 (p0) REVERT: A 203 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7683 (t70) REVERT: A 271 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7600 (mp10) REVERT: B 226 LEU cc_start: 0.8764 (mt) cc_final: 0.8558 (mt) REVERT: B 243 HIS cc_start: 0.8465 (t-90) cc_final: 0.8256 (t70) REVERT: B 348 GLU cc_start: 0.8276 (tp30) cc_final: 0.7994 (tt0) REVERT: B 565 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (mt) outliers start: 17 outliers final: 9 residues processed: 175 average time/residue: 0.1244 time to fit residues: 30.8844 Evaluate side-chains 149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 475 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: 0.5980 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: 4.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 601 ASN F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103462 restraints weight = 16530.802| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.70 r_work: 0.2894 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12735 Z= 0.228 Angle : 0.699 8.967 17280 Z= 0.350 Chirality : 0.046 0.191 1972 Planarity : 0.005 0.044 2144 Dihedral : 10.289 129.948 1874 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.85 % Allowed : 8.37 % Favored : 89.78 % 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: -1.36 (0.20), residues: 1558 helix: -0.26 (0.20), residues: 672 sheet: -0.40 (0.32), residues: 274 loop : -1.78 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 32 TYR 0.023 0.002 TYR A 570 PHE 0.033 0.002 PHE B 293 TRP 0.012 0.002 TRP F 109 HIS 0.006 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00560 (12724) covalent geometry : angle 0.69493 (17254) SS BOND : bond 0.00688 ( 7) SS BOND : angle 1.73877 ( 14) hydrogen bonds : bond 0.05002 ( 534) hydrogen bonds : angle 4.49276 ( 1572) link_BETA1-4 : bond 0.00793 ( 2) link_BETA1-4 : angle 2.26142 ( 6) link_NAG-ASN : bond 0.00270 ( 2) link_NAG-ASN : angle 2.28653 ( 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 163 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.490 Fit side-chains REVERT: A 127 ASP cc_start: 0.7696 (p0) cc_final: 0.7272 (p0) REVERT: A 203 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7627 (t70) REVERT: A 220 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7166 (t) REVERT: A 271 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7629 (mp10) REVERT: B 226 LEU cc_start: 0.8757 (mt) cc_final: 0.8549 (mt) REVERT: B 243 HIS cc_start: 0.8589 (t-90) cc_final: 0.8284 (t70) REVERT: B 348 GLU cc_start: 0.8270 (tp30) cc_final: 0.8041 (tt0) outliers start: 25 outliers final: 20 residues processed: 160 average time/residue: 0.1184 time to fit residues: 27.5888 Evaluate side-chains 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 36 ASN Chi-restraints excluded: chain D residue 81 LEU 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: 0.2980 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.133778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106263 restraints weight = 16346.628| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.60 r_work: 0.2953 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2699 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= 0.138 Angle : 0.603 7.955 17280 Z= 0.305 Chirality : 0.043 0.141 1972 Planarity : 0.004 0.039 2144 Dihedral : 9.979 128.462 1874 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.63 % Allowed : 9.11 % Favored : 89.26 % 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: -0.76 (0.21), residues: 1558 helix: 0.48 (0.21), residues: 662 sheet: -0.37 (0.32), residues: 278 loop : -1.62 (0.23), residues: 618 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 0.033 0.002 PHE A 293 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00328 (12724) covalent geometry : angle 0.59959 (17254) SS BOND : bond 0.00515 ( 7) SS BOND : angle 1.26919 ( 14) hydrogen bonds : bond 0.03973 ( 534) hydrogen bonds : angle 4.19048 ( 1572) link_BETA1-4 : bond 0.00741 ( 2) link_BETA1-4 : angle 2.32418 ( 6) link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 2.03104 ( 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 156 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.491 Fit side-chains REVERT: A 127 ASP cc_start: 0.7692 (p0) cc_final: 0.7254 (p0) REVERT: A 203 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7649 (t70) REVERT: A 220 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7211 (t) REVERT: A 271 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7687 (mp10) REVERT: B 226 LEU cc_start: 0.8739 (mt) cc_final: 0.8538 (mt) REVERT: B 243 HIS cc_start: 0.8689 (t-90) cc_final: 0.8366 (t70) REVERT: B 348 GLU cc_start: 0.8393 (tp30) cc_final: 0.8130 (tt0) REVERT: B 502 LYS cc_start: 0.8280 (mmtt) cc_final: 0.8056 (mptt) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 0.1148 time to fit residues: 26.0145 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 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 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 A residue 587 LEU Chi-restraints excluded: chain B residue 87 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 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: 8.9990 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: 0.8980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 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 = 0.3596 r_free = 0.3596 target = 0.130028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102831 restraints weight = 16613.141| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.76 r_work: 0.2853 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12735 Z= 0.292 Angle : 0.735 8.836 17280 Z= 0.365 Chirality : 0.049 0.244 1972 Planarity : 0.005 0.039 2144 Dihedral : 10.147 123.789 1874 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.52 % Allowed : 9.11 % Favored : 88.37 % 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: -0.78 (0.21), residues: 1558 helix: 0.46 (0.21), residues: 664 sheet: -0.26 (0.33), residues: 274 loop : -1.67 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 67 TYR 0.019 0.002 TYR A 570 PHE 0.032 0.002 PHE A 293 TRP 0.011 0.003 TRP C 35 HIS 0.007 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00721 (12724) covalent geometry : angle 0.73093 (17254) SS BOND : bond 0.00793 ( 7) SS BOND : angle 2.01976 ( 14) hydrogen bonds : bond 0.04942 ( 534) hydrogen bonds : angle 4.40953 ( 1572) link_BETA1-4 : bond 0.01136 ( 2) link_BETA1-4 : angle 2.22539 ( 6) link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 2.39376 ( 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 166 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.456 Fit side-chains REVERT: A 127 ASP cc_start: 0.7672 (p0) cc_final: 0.6946 (p0) REVERT: A 220 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7163 (t) REVERT: A 271 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7678 (mp10) REVERT: B 127 ASP cc_start: 0.7925 (p0) cc_final: 0.7349 (p0) REVERT: B 614 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9281 (mp) REVERT: D 47 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8324 (tt0) outliers start: 34 outliers final: 25 residues processed: 164 average time/residue: 0.1155 time to fit residues: 27.6609 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 : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS 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 340 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 17 SER 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 91 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 17 SER 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: 4.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 112 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 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 = 0.3636 r_free = 0.3636 target = 0.133580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106182 restraints weight = 16595.331| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.79 r_work: 0.2927 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3037 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= 0.118 Angle : 0.586 7.791 17280 Z= 0.298 Chirality : 0.042 0.194 1972 Planarity : 0.003 0.041 2144 Dihedral : 9.721 121.948 1874 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.22 % Allowed : 9.93 % Favored : 87.85 % 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: -0.32 (0.22), residues: 1558 helix: 1.00 (0.21), residues: 666 sheet: -0.27 (0.32), residues: 280 loop : -1.54 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.016 0.001 TYR A 342 PHE 0.033 0.002 PHE A 293 TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00277 (12724) covalent geometry : angle 0.58213 (17254) SS BOND : bond 0.00402 ( 7) SS BOND : angle 1.10665 ( 14) hydrogen bonds : bond 0.03615 ( 534) hydrogen bonds : angle 4.07025 ( 1572) link_BETA1-4 : bond 0.00649 ( 2) link_BETA1-4 : angle 2.42695 ( 6) link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 2.11066 ( 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 164 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.318 Fit side-chains REVERT: A 127 ASP cc_start: 0.7535 (p0) cc_final: 0.7130 (p0) REVERT: B 127 ASP cc_start: 0.7886 (p0) cc_final: 0.7323 (p0) outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 0.1090 time to fit residues: 26.2720 Evaluate side-chains 141 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 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 = 0.3642 r_free = 0.3642 target = 0.133680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105973 restraints weight = 16441.355| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.70 r_work: 0.2948 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3148 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= 0.122 Angle : 0.591 7.423 17280 Z= 0.296 Chirality : 0.042 0.185 1972 Planarity : 0.003 0.042 2144 Dihedral : 9.460 120.861 1874 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.00 % Allowed : 9.78 % 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: 0.00 (0.22), residues: 1558 helix: 1.30 (0.21), residues: 666 sheet: -0.20 (0.32), residues: 278 loop : -1.34 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.019 0.001 TYR B 342 PHE 0.033 0.002 PHE A 293 TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00288 (12724) covalent geometry : angle 0.58749 (17254) SS BOND : bond 0.00463 ( 7) SS BOND : angle 1.24882 ( 14) hydrogen bonds : bond 0.03532 ( 534) hydrogen bonds : angle 3.96351 ( 1572) link_BETA1-4 : bond 0.00800 ( 2) link_BETA1-4 : angle 2.21776 ( 6) link_NAG-ASN : bond 0.00250 ( 2) link_NAG-ASN : angle 2.17638 ( 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: 27 poor density : 126 time to evaluate : 0.494 Fit side-chains REVERT: A 127 ASP cc_start: 0.7600 (p0) cc_final: 0.7178 (p0) REVERT: B 127 ASP cc_start: 0.8044 (p0) cc_final: 0.7241 (p0) outliers start: 27 outliers final: 24 residues processed: 151 average time/residue: 0.1145 time to fit residues: 25.1526 Evaluate side-chains 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 218 SER Chi-restraints excluded: chain B residue 340 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 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: 0.2980 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3628 r_free = 0.3628 target = 0.132573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104392 restraints weight = 16364.941| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.63 r_work: 0.2939 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12735 Z= 0.159 Angle : 0.623 7.814 17280 Z= 0.312 Chirality : 0.044 0.274 1972 Planarity : 0.004 0.040 2144 Dihedral : 9.363 119.194 1874 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.00 % Allowed : 10.15 % Favored : 87.85 % 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: 0.03 (0.22), residues: 1558 helix: 1.32 (0.21), residues: 666 sheet: -0.17 (0.32), residues: 278 loop : -1.34 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.017 0.002 TYR B 342 PHE 0.034 0.002 PHE A 293 TRP 0.009 0.002 TRP B 379 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00388 (12724) covalent geometry : angle 0.61924 (17254) SS BOND : bond 0.00540 ( 7) SS BOND : angle 1.47609 ( 14) hydrogen bonds : bond 0.03831 ( 534) hydrogen bonds : angle 4.04529 ( 1572) link_BETA1-4 : bond 0.00847 ( 2) link_BETA1-4 : angle 2.17318 ( 6) link_NAG-ASN : bond 0.00311 ( 2) link_NAG-ASN : angle 2.25772 ( 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 153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.336 Fit side-chains REVERT: A 127 ASP cc_start: 0.7559 (p0) cc_final: 0.7230 (p0) REVERT: A 349 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6531 (mp) REVERT: B 127 ASP cc_start: 0.7912 (p0) cc_final: 0.7353 (p0) outliers start: 27 outliers final: 24 residues processed: 151 average time/residue: 0.1146 time to fit residues: 25.3321 Evaluate side-chains 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 340 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 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=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: 4.9990 chunk 88 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 50 optimal weight: 0.0980 chunk 17 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 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 = 0.3658 r_free = 0.3658 target = 0.134986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107559 restraints weight = 16349.873| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.61 r_work: 0.2986 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12735 Z= 0.100 Angle : 0.579 10.609 17280 Z= 0.293 Chirality : 0.042 0.356 1972 Planarity : 0.003 0.038 2144 Dihedral : 9.079 118.428 1874 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.78 % Allowed : 10.22 % Favored : 88.00 % 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: 0.26 (0.22), residues: 1558 helix: 1.56 (0.21), residues: 666 sheet: -0.14 (0.32), residues: 282 loop : -1.22 (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 B 342 PHE 0.035 0.001 PHE B 293 TRP 0.011 0.001 TRP D 35 HIS 0.009 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00218 (12724) covalent geometry : angle 0.57583 (17254) SS BOND : bond 0.00340 ( 7) SS BOND : angle 1.14675 ( 14) hydrogen bonds : bond 0.03307 ( 534) hydrogen bonds : angle 3.92273 ( 1572) link_BETA1-4 : bond 0.00661 ( 2) link_BETA1-4 : angle 2.22542 ( 6) link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 2.13350 ( 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 155 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.547 Fit side-chains REVERT: A 127 ASP cc_start: 0.7546 (p0) cc_final: 0.7113 (p0) REVERT: A 349 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6372 (mp) REVERT: B 127 ASP cc_start: 0.7845 (p0) cc_final: 0.7291 (p0) REVERT: B 271 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8313 (pt0) REVERT: D 47 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8430 (tt0) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.1165 time to fit residues: 26.0050 Evaluate side-chains 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 340 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 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: 1.9990 chunk 112 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 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 = 0.3653 r_free = 0.3653 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106822 restraints weight = 16513.532| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.67 r_work: 0.2964 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3330 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= 0.117 Angle : 0.600 12.237 17280 Z= 0.299 Chirality : 0.043 0.313 1972 Planarity : 0.003 0.045 2144 Dihedral : 8.943 117.375 1874 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: 0.35 (0.22), residues: 1558 helix: 1.61 (0.21), residues: 666 sheet: -0.08 (0.32), residues: 282 loop : -1.16 (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 0.039 0.002 PHE B 293 TRP 0.009 0.001 TRP A 379 HIS 0.009 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00271 (12724) covalent geometry : angle 0.59676 (17254) SS BOND : bond 0.00409 ( 7) SS BOND : angle 1.25988 ( 14) hydrogen bonds : bond 0.03353 ( 534) hydrogen bonds : angle 3.91064 ( 1572) link_BETA1-4 : bond 0.00817 ( 2) link_BETA1-4 : angle 2.11803 ( 6) link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 2.17707 ( 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 154 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.533 Fit side-chains REVERT: A 127 ASP cc_start: 0.7525 (p0) cc_final: 0.7080 (p0) REVERT: A 349 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6255 (mp) REVERT: B 127 ASP cc_start: 0.7881 (p0) cc_final: 0.7341 (p0) REVERT: B 271 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8307 (pt0) REVERT: D 47 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8432 (tt0) outliers start: 24 outliers final: 21 residues processed: 151 average time/residue: 0.1066 time to fit residues: 23.8809 Evaluate side-chains 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 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 349 LEU Chi-restraints excluded: chain A residue 371 THR 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 340 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 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: 0.8980 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 601 ASN D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107367 restraints weight = 16392.720| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.66 r_work: 0.2962 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3375 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 : 0.595 11.289 17280 Z= 0.297 Chirality : 0.042 0.290 1972 Planarity : 0.003 0.040 2144 Dihedral : 8.756 115.583 1874 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.85 % Allowed : 10.30 % Favored : 87.85 % 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: 0.43 (0.22), residues: 1558 helix: 1.67 (0.21), residues: 666 sheet: -0.02 (0.32), residues: 282 loop : -1.11 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 575 TYR 0.018 0.001 TYR A 342 PHE 0.039 0.002 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.009 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00264 (12724) covalent geometry : angle 0.59163 (17254) SS BOND : bond 0.00404 ( 7) SS BOND : angle 1.15098 ( 14) hydrogen bonds : bond 0.03343 ( 534) hydrogen bonds : angle 3.87615 ( 1572) link_BETA1-4 : bond 0.00777 ( 2) link_BETA1-4 : angle 2.09203 ( 6) link_NAG-ASN : bond 0.00289 ( 2) link_NAG-ASN : angle 2.15898 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.64 seconds wall clock time: 51 minutes 13.61 seconds (3073.61 seconds total)