Starting phenix.real_space_refine on Wed Jul 30 19:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eti_3953/07_2025/6eti_3953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eti_3953/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6eti_3953/07_2025/6eti_3953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eti_3953/07_2025/6eti_3953.map" model { file = "/net/cci-nas-00/data/ceres_data/6eti_3953/07_2025/6eti_3953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eti_3953/07_2025/6eti_3953.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.53, per 1000 atoms: 0.61 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.36 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: 3.63 Time building geometry restraints manager: 3.21 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: 0.06 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.004 TRP E 96 HIS 0.011 0.003 HIS B 457 PHE 0.048 0.004 PHE E 98 TYR 0.042 0.004 TYR A 570 ARG 0.009 0.002 ARG B 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 2) link_NAG-ASN : angle 5.81929 ( 6) link_BETA1-4 : bond 0.01934 ( 2) link_BETA1-4 : angle 4.69425 ( 6) hydrogen bonds : bond 0.30306 ( 534) hydrogen bonds : angle 9.70086 ( 1572) SS BOND : bond 0.00853 ( 7) SS BOND : angle 2.70584 ( 14) covalent geometry : bond 0.01046 (12724) covalent geometry : angle 1.09036 (17254) *********************** 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 : 1.388 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: 0.2980 time to fit residues: 92.2566 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3682 r_free = 0.3682 target = 0.136863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108772 restraints weight = 16275.654| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.60 r_work: 0.2996 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12735 Z= 0.149 Angle : 0.668 8.703 17280 Z= 0.341 Chirality : 0.043 0.156 1972 Planarity : 0.005 0.044 2144 Dihedral : 10.467 131.930 1874 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.19), residues: 1558 helix: -1.72 (0.17), residues: 666 sheet: -0.72 (0.31), residues: 272 loop : -1.90 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 109 HIS 0.006 0.001 HIS B 40 PHE 0.041 0.002 PHE A 293 TYR 0.017 0.002 TYR A 570 ARG 0.003 0.001 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 2) link_NAG-ASN : angle 2.27910 ( 6) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 2.37096 ( 6) hydrogen bonds : bond 0.05228 ( 534) hydrogen bonds : angle 4.84102 ( 1572) SS BOND : bond 0.00539 ( 7) SS BOND : angle 1.23610 ( 14) covalent geometry : bond 0.00343 (12724) covalent geometry : angle 0.66498 (17254) *********************** 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 177 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (t70) REVERT: A 271 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7720 (mp10) REVERT: B 226 LEU cc_start: 0.8791 (mt) cc_final: 0.8583 (mt) REVERT: B 243 HIS cc_start: 0.8592 (t-90) cc_final: 0.8376 (t70) REVERT: B 348 GLU cc_start: 0.8438 (tp30) cc_final: 0.8074 (tt0) REVERT: B 565 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 600 ASN cc_start: 0.6321 (t0) cc_final: 0.6074 (t0) outliers start: 17 outliers final: 9 residues processed: 172 average time/residue: 0.2664 time to fit residues: 65.1439 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 : 1.393 ------------------------------------------------------------------------------- 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 107 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.133939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105314 restraints weight = 16458.566| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.65 r_work: 0.2935 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12735 Z= 0.167 Angle : 0.644 7.969 17280 Z= 0.325 Chirality : 0.044 0.165 1972 Planarity : 0.004 0.039 2144 Dihedral : 10.200 131.406 1874 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.56 % Allowed : 8.74 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1558 helix: -0.23 (0.19), residues: 672 sheet: -0.42 (0.32), residues: 274 loop : -1.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 109 HIS 0.006 0.002 HIS A 243 PHE 0.033 0.002 PHE B 293 TYR 0.018 0.002 TYR A 570 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 2.11548 ( 6) link_BETA1-4 : bond 0.00784 ( 2) link_BETA1-4 : angle 2.30251 ( 6) hydrogen bonds : bond 0.04645 ( 534) hydrogen bonds : angle 4.39499 ( 1572) SS BOND : bond 0.00555 ( 7) SS BOND : angle 1.45360 ( 14) covalent geometry : bond 0.00405 (12724) covalent geometry : angle 0.64002 (17254) *********************** 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 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7915 (p0) cc_final: 0.7391 (p0) REVERT: A 203 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7694 (t70) REVERT: A 220 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7206 (t) REVERT: A 271 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7664 (mp10) REVERT: B 226 LEU cc_start: 0.8783 (mt) cc_final: 0.8569 (mt) REVERT: B 243 HIS cc_start: 0.8688 (t-90) cc_final: 0.8396 (t70) REVERT: B 348 GLU cc_start: 0.8439 (tp30) cc_final: 0.8116 (tt0) REVERT: B 600 ASN cc_start: 0.6283 (t0) cc_final: 0.6063 (t0) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 0.3204 time to fit residues: 75.5141 Evaluate side-chains 143 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103514 restraints weight = 16280.207| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.71 r_work: 0.2893 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12735 Z= 0.227 Angle : 0.687 8.104 17280 Z= 0.344 Chirality : 0.046 0.187 1972 Planarity : 0.004 0.038 2144 Dihedral : 10.156 129.034 1874 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.93 % Allowed : 8.89 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1558 helix: 0.31 (0.20), residues: 664 sheet: -0.35 (0.32), residues: 278 loop : -1.69 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 109 HIS 0.005 0.002 HIS A 630 PHE 0.033 0.002 PHE B 293 TYR 0.022 0.002 TYR B 570 ARG 0.004 0.001 ARG B 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 2) link_NAG-ASN : angle 2.25476 ( 6) link_BETA1-4 : bond 0.00837 ( 2) link_BETA1-4 : angle 2.24511 ( 6) hydrogen bonds : bond 0.04658 ( 534) hydrogen bonds : angle 4.34980 ( 1572) SS BOND : bond 0.00661 ( 7) SS BOND : angle 1.80885 ( 14) covalent geometry : bond 0.00559 (12724) covalent geometry : angle 0.68274 (17254) *********************** 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 159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.675 Fit side-chains REVERT: A 127 ASP cc_start: 0.7946 (p0) cc_final: 0.7416 (p0) REVERT: A 203 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7671 (t70) REVERT: A 220 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7251 (t) REVERT: A 271 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7713 (mp10) REVERT: B 348 GLU cc_start: 0.8411 (tp30) cc_final: 0.8154 (tt0) REVERT: B 502 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8174 (mptt) REVERT: B 600 ASN cc_start: 0.6069 (t0) cc_final: 0.5699 (t0) outliers start: 26 outliers final: 20 residues processed: 157 average time/residue: 0.2471 time to fit residues: 57.4771 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 237 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 237 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 514 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101930 restraints weight = 16656.443| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.90 r_work: 0.2850 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12735 Z= 0.199 Angle : 0.647 7.611 17280 Z= 0.326 Chirality : 0.045 0.171 1972 Planarity : 0.004 0.038 2144 Dihedral : 10.081 129.711 1874 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.04 % Allowed : 8.96 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1558 helix: 0.67 (0.21), residues: 662 sheet: -0.28 (0.32), residues: 278 loop : -1.59 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 379 HIS 0.008 0.001 HIS B 243 PHE 0.033 0.002 PHE B 293 TYR 0.015 0.002 TYR B 570 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 2.27095 ( 6) link_BETA1-4 : bond 0.00848 ( 2) link_BETA1-4 : angle 2.29712 ( 6) hydrogen bonds : bond 0.04288 ( 534) hydrogen bonds : angle 4.24714 ( 1572) SS BOND : bond 0.00625 ( 7) SS BOND : angle 1.60100 ( 14) covalent geometry : bond 0.00491 (12724) covalent geometry : angle 0.64338 (17254) *********************** 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 168 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.413 Fit side-chains REVERT: A 127 ASP cc_start: 0.7650 (p0) cc_final: 0.7211 (p0) REVERT: A 271 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7670 (mp10) REVERT: B 127 ASP cc_start: 0.7910 (p0) cc_final: 0.7366 (p0) REVERT: B 348 GLU cc_start: 0.8307 (tp30) cc_final: 0.8097 (tt0) REVERT: B 446 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B 600 ASN cc_start: 0.6013 (t0) cc_final: 0.5704 (t0) REVERT: D 47 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8326 (tt0) outliers start: 41 outliers final: 23 residues processed: 166 average time/residue: 0.2441 time to fit residues: 59.3631 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 218 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 371 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 chunk 87 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105383 restraints weight = 16538.029| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.53 r_work: 0.2962 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12735 Z= 0.118 Angle : 0.579 8.020 17280 Z= 0.292 Chirality : 0.042 0.140 1972 Planarity : 0.003 0.040 2144 Dihedral : 9.886 131.277 1874 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 9.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1558 helix: 1.08 (0.21), residues: 666 sheet: -0.26 (0.32), residues: 280 loop : -1.43 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS B 40 PHE 0.034 0.001 PHE B 293 TYR 0.014 0.001 TYR A 342 ARG 0.004 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 2) link_NAG-ASN : angle 2.13639 ( 6) link_BETA1-4 : bond 0.00627 ( 2) link_BETA1-4 : angle 2.35761 ( 6) hydrogen bonds : bond 0.03584 ( 534) hydrogen bonds : angle 4.02256 ( 1572) SS BOND : bond 0.00450 ( 7) SS BOND : angle 1.14121 ( 14) covalent geometry : bond 0.00277 (12724) covalent geometry : angle 0.57520 (17254) *********************** 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 163 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.249 Fit side-chains REVERT: A 127 ASP cc_start: 0.7676 (p0) cc_final: 0.6895 (p0) REVERT: A 271 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8242 (pt0) REVERT: B 127 ASP cc_start: 0.7963 (p0) cc_final: 0.7134 (p0) REVERT: B 600 ASN cc_start: 0.6200 (t0) cc_final: 0.5784 (t0) outliers start: 28 outliers final: 21 residues processed: 159 average time/residue: 0.2498 time to fit residues: 58.9124 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 172 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 122 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106497 restraints weight = 16390.223| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.54 r_work: 0.2987 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3181 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= 0.109 Angle : 0.576 7.749 17280 Z= 0.291 Chirality : 0.041 0.170 1972 Planarity : 0.003 0.043 2144 Dihedral : 9.755 132.545 1874 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.85 % Allowed : 10.22 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1558 helix: 1.39 (0.21), residues: 666 sheet: -0.22 (0.32), residues: 282 loop : -1.35 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS B 243 PHE 0.034 0.001 PHE B 293 TYR 0.013 0.001 TYR A 342 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 2) link_NAG-ASN : angle 2.12076 ( 6) link_BETA1-4 : bond 0.00758 ( 2) link_BETA1-4 : angle 2.24426 ( 6) hydrogen bonds : bond 0.03400 ( 534) hydrogen bonds : angle 3.93250 ( 1572) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.10084 ( 14) covalent geometry : bond 0.00252 (12724) covalent geometry : angle 0.57266 (17254) *********************** 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 156 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.343 Fit side-chains REVERT: A 120 ASN cc_start: 0.7570 (m-40) cc_final: 0.7279 (m-40) REVERT: A 127 ASP cc_start: 0.7564 (p0) cc_final: 0.7084 (p0) REVERT: B 127 ASP cc_start: 0.7833 (p0) cc_final: 0.7375 (p0) REVERT: B 600 ASN cc_start: 0.6159 (t0) cc_final: 0.5795 (t0) REVERT: D 47 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8394 (tt0) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.2417 time to fit residues: 53.7789 Evaluate side-chains 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103329 restraints weight = 16530.693| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.78 r_work: 0.2891 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12735 Z= 0.198 Angle : 0.655 8.173 17280 Z= 0.327 Chirality : 0.045 0.209 1972 Planarity : 0.004 0.039 2144 Dihedral : 9.867 131.888 1874 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.93 % Allowed : 10.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1558 helix: 1.29 (0.21), residues: 664 sheet: -0.17 (0.32), residues: 282 loop : -1.38 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 379 HIS 0.008 0.001 HIS A 243 PHE 0.033 0.002 PHE A 293 TYR 0.015 0.002 TYR F 51 ARG 0.004 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 2) link_NAG-ASN : angle 2.31330 ( 6) link_BETA1-4 : bond 0.00870 ( 2) link_BETA1-4 : angle 2.12086 ( 6) hydrogen bonds : bond 0.04095 ( 534) hydrogen bonds : angle 4.11117 ( 1572) SS BOND : bond 0.00604 ( 7) SS BOND : angle 1.64055 ( 14) covalent geometry : bond 0.00487 (12724) covalent geometry : angle 0.65125 (17254) *********************** 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 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.429 Fit side-chains REVERT: A 127 ASP cc_start: 0.7411 (p0) cc_final: 0.6951 (p0) REVERT: B 127 ASP cc_start: 0.7730 (p0) cc_final: 0.7195 (p0) REVERT: B 600 ASN cc_start: 0.6009 (t0) cc_final: 0.5748 (t0) REVERT: D 47 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8277 (tt0) outliers start: 26 outliers final: 25 residues processed: 149 average time/residue: 0.2468 time to fit residues: 54.2425 Evaluate side-chains 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 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 81 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102490 restraints weight = 16561.935| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.88 r_work: 0.2866 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12735 Z= 0.240 Angle : 0.701 8.420 17280 Z= 0.348 Chirality : 0.047 0.271 1972 Planarity : 0.004 0.038 2144 Dihedral : 9.900 131.252 1874 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.30 % Allowed : 9.85 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1558 helix: 1.07 (0.21), residues: 668 sheet: -0.16 (0.32), residues: 276 loop : -1.39 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 35 HIS 0.010 0.002 HIS B 243 PHE 0.037 0.002 PHE B 293 TYR 0.015 0.002 TYR D 51 ARG 0.004 0.000 ARG C 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 2.38230 ( 6) link_BETA1-4 : bond 0.00946 ( 2) link_BETA1-4 : angle 2.15894 ( 6) hydrogen bonds : bond 0.04440 ( 534) hydrogen bonds : angle 4.24856 ( 1572) SS BOND : bond 0.00668 ( 7) SS BOND : angle 1.83634 ( 14) covalent geometry : bond 0.00591 (12724) covalent geometry : angle 0.69699 (17254) *********************** 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 158 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.332 Fit side-chains REVERT: A 127 ASP cc_start: 0.7422 (p0) cc_final: 0.6992 (p0) REVERT: A 349 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6791 (mp) REVERT: B 127 ASP cc_start: 0.7751 (p0) cc_final: 0.7246 (p0) REVERT: B 600 ASN cc_start: 0.5864 (t0) cc_final: 0.5540 (t0) REVERT: D 47 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: F 47 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8281 (tt0) outliers start: 31 outliers final: 27 residues processed: 154 average time/residue: 0.2379 time to fit residues: 53.6265 Evaluate side-chains 154 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 153 THR 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 87 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 109 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104951 restraints weight = 16386.661| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.56 r_work: 0.2961 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12735 Z= 0.124 Angle : 0.612 11.642 17280 Z= 0.305 Chirality : 0.043 0.305 1972 Planarity : 0.003 0.038 2144 Dihedral : 9.737 133.516 1874 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.07 % Allowed : 10.30 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1558 helix: 1.38 (0.21), residues: 666 sheet: -0.17 (0.32), residues: 280 loop : -1.24 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.013 0.001 HIS B 243 PHE 0.036 0.002 PHE B 293 TYR 0.015 0.001 TYR A 342 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 2) link_NAG-ASN : angle 2.23888 ( 6) link_BETA1-4 : bond 0.00832 ( 2) link_BETA1-4 : angle 2.31180 ( 6) hydrogen bonds : bond 0.03551 ( 534) hydrogen bonds : angle 4.03047 ( 1572) SS BOND : bond 0.00401 ( 7) SS BOND : angle 1.20006 ( 14) covalent geometry : bond 0.00294 (12724) covalent geometry : angle 0.60852 (17254) ********************** 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 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.377 Fit side-chains REVERT: A 127 ASP cc_start: 0.7503 (p0) cc_final: 0.7181 (p0) REVERT: A 349 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6481 (mp) REVERT: B 127 ASP cc_start: 0.7812 (p0) cc_final: 0.7295 (p0) REVERT: B 271 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8311 (pt0) REVERT: B 600 ASN cc_start: 0.6165 (t0) cc_final: 0.5896 (t0) REVERT: D 47 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: F 47 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8418 (tt0) outliers start: 28 outliers final: 25 residues processed: 157 average time/residue: 0.3028 time to fit residues: 70.9013 Evaluate side-chains 155 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 34 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104659 restraints weight = 16383.466| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.63 r_work: 0.2932 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12735 Z= 0.140 Angle : 0.626 11.556 17280 Z= 0.311 Chirality : 0.044 0.294 1972 Planarity : 0.003 0.038 2144 Dihedral : 9.690 133.630 1874 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.15 % Allowed : 10.37 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1558 helix: 1.44 (0.21), residues: 666 sheet: -0.12 (0.32), residues: 280 loop : -1.16 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.035 0.002 PHE A 293 TYR 0.014 0.001 TYR A 342 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 2) link_NAG-ASN : angle 2.29223 ( 6) link_BETA1-4 : bond 0.00816 ( 2) link_BETA1-4 : angle 2.19288 ( 6) hydrogen bonds : bond 0.03636 ( 534) hydrogen bonds : angle 4.00416 ( 1572) SS BOND : bond 0.00506 ( 7) SS BOND : angle 1.44314 ( 14) covalent geometry : bond 0.00337 (12724) covalent geometry : angle 0.62193 (17254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6648.52 seconds wall clock time: 117 minutes 30.22 seconds (7050.22 seconds total)