Starting phenix.real_space_refine on Sat Sep 12 00:18:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nfd_12300/09_2026/7nfd_12300.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 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 7998 2.51 5 N 2040 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12394 Number of models: 1 Model: "" Number of chains: 9 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: "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: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 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: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'MIX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.21 Number of scatterers: 12394 At special positions: 0 Unit cell: (100.32, 98.34, 147.18, 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 2288 8.00 N 2040 7.00 C 7998 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=2.05 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 475.6 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 16 sheets defined 42.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.717A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.543A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.807A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.328A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 289 through 300 removed outlier: 4.559A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.365A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 339 through 353 removed outlier: 4.347A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 4.101A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 413 Processing helix chain 'A' and resid 419 through 440 removed outlier: 4.116A pdb=" N ILE A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.848A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 4.502A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.528A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.538A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.698A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.645A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.546A pdb=" N MET A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.669A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 4.096A 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 'D' and resid 73 through 76 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.669A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 4.095A 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 helix chain 'F' and resid 73 through 76 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.717A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.542A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.807A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 4.330A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 289 through 300 removed outlier: 4.558A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.365A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 339 through 353 removed outlier: 4.346A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.100A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 413 Processing helix chain 'B' and resid 419 through 440 removed outlier: 4.115A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.742A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.848A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 4.502A pdb=" N MET B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.528A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.540A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.697A pdb=" N GLN B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.645A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 650 removed outlier: 3.546A pdb=" N MET B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.529A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 239 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.089A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.946A pdb=" N ARG C 45 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'E' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.947A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 23 Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.528A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 239 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 258 through 260 removed outlier: 6.089A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1281 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: 1.27 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1934 1.28 - 1.42: 3372 1.42 - 1.55: 7248 1.55 - 1.68: 10 1.68 - 1.81: 106 Bond restraints: 12670 Sorted by residual: bond pdb=" C PHE B 432 " pdb=" O PHE B 432 " ideal model delta sigma weight residual 1.236 1.150 0.085 1.29e-02 6.01e+03 4.38e+01 bond pdb=" C VAL B 546 " pdb=" O VAL B 546 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.19e-02 7.06e+03 3.82e+01 bond pdb=" CA ASN A 436 " pdb=" CB ASN A 436 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.56e-02 4.11e+03 3.00e+01 bond pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 1.237 1.178 0.058 1.19e-02 7.06e+03 2.41e+01 bond pdb=" C PHE B 432 " pdb=" N LEU B 433 " ideal model delta sigma weight residual 1.334 1.269 0.065 1.41e-02 5.03e+03 2.12e+01 ... (remaining 12665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 16635 2.51 - 5.03: 466 5.03 - 7.54: 43 7.54 - 10.06: 14 10.06 - 12.57: 8 Bond angle restraints: 17166 Sorted by residual: angle pdb=" CA THR A 435 " pdb=" CB THR A 435 " pdb=" OG1 THR A 435 " ideal model delta sigma weight residual 109.60 97.03 12.57 1.50e+00 4.44e-01 7.02e+01 angle pdb=" CA THR A 542 " pdb=" CB THR A 542 " pdb=" OG1 THR A 542 " ideal model delta sigma weight residual 109.60 98.27 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" C ASN B 436 " pdb=" CA ASN B 436 " pdb=" CB ASN B 436 " ideal model delta sigma weight residual 110.79 100.32 10.47 1.68e+00 3.54e-01 3.89e+01 angle pdb=" CA MET B 549 " pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 120.42 114.19 6.23 1.06e+00 8.90e-01 3.46e+01 angle pdb=" CA THR B 542 " pdb=" CB THR B 542 " pdb=" OG1 THR B 542 " ideal model delta sigma weight residual 109.60 101.46 8.14 1.50e+00 4.44e-01 2.94e+01 ... (remaining 17161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6614 17.96 - 35.92: 662 35.92 - 53.88: 109 53.88 - 71.84: 18 71.84 - 89.80: 12 Dihedral angle restraints: 7415 sinusoidal: 2879 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LYS A 233 " pdb=" C LYS A 233 " pdb=" N GLN A 234 " pdb=" CA GLN A 234 " ideal model delta harmonic sigma weight residual 180.00 137.29 42.71 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA LYS B 233 " pdb=" C LYS B 233 " pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta harmonic sigma weight residual 180.00 137.32 42.68 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 7412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1617 0.069 - 0.138: 314 0.138 - 0.206: 27 0.206 - 0.275: 1 0.275 - 0.344: 5 Chirality restraints: 1964 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.49e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.33e+01 chirality pdb=" CA PHE B 432 " pdb=" N PHE B 432 " pdb=" C PHE B 432 " pdb=" CB PHE B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1961 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 442 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C VAL A 442 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 442 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 443 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 439 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C PHE B 439 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 440 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 436 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" CG ASN A 436 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 436 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 264 2.64 - 3.20: 12492 3.20 - 3.77: 18107 3.77 - 4.33: 25509 4.33 - 4.90: 42508 Nonbonded interactions: 98880 Sorted by model distance: nonbonded pdb=" CD1 TYR A 287 " pdb=" CD1 TYR B 287 " model vdw 2.071 3.640 nonbonded pdb=" NH1 ARG C 61 " pdb=" OD2 ASP C 82 " model vdw 2.082 3.120 nonbonded pdb=" ND2 ASN A 68 " pdb=" NZ LYS A 346 " model vdw 2.186 3.200 nonbonded pdb=" NAV MIX B1201 " pdb=" OAB MIX B1201 " model vdw 2.197 3.120 nonbonded pdb=" NE2 GLN C 89 " pdb=" O GLN C 90 " model vdw 2.199 3.120 ... (remaining 98875 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 35 through 654) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.840 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.009 0.085 12681 Z= 0.440 Angle : 1.336 60.353 17192 Z= 0.637 Chirality : 0.055 0.344 1964 Planarity : 0.005 0.044 2133 Dihedral : 14.732 89.803 4498 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.92 % Favored : 83.95 % Rotamer: Outliers : 0.37 % Allowed : 0.00 % Favored : 99.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.50 (0.16), residues: 1558 helix: -2.76 (0.16), residues: 642 sheet: -3.65 (0.33), residues: 198 loop : -4.56 (0.17), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 246 TYR 0.019 0.002 TYR E 91 PHE 0.035 0.003 PHE B 432 TRP 0.009 0.002 TRP E 92 HIS 0.006 0.002 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.44 (12670) covalent geometry : angle 1.01630 / 0.57 (17166) SS BOND : bond 0.01050 / 0.72 ( 7) SS BOND : angle 2.78388 / 1.42 ( 14) hydrogen bonds : bond 0.16545 / 10.80 ( 444) hydrogen bonds : angle 7.17437 / 4.93 ( 1281) link_BETA1-4 : bond 0.06574 / 3.30 ( 2) link_BETA1-4 : angle 46.07313 / 29.27 ( 6) link_NAG-ASN : bond 0.00630 / 0.32 ( 2) link_NAG-ASN : angle 4.00821 / 2.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 280 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.7514 (m-40) cc_final: 0.7071 (p0) REVERT: A 96 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.8073 (tpp80) REVERT: A 127 ASP cc_start: 0.7706 (p0) cc_final: 0.7207 (p0) REVERT: A 465 ARG cc_start: 0.6257 (ptp-110) cc_final: 0.5865 (mmt-90) REVERT: A 481 MET cc_start: 0.7616 (tpt) cc_final: 0.6682 (ttp) REVERT: A 515 MET cc_start: 0.8892 (mmm) cc_final: 0.8611 (mmp) REVERT: C 24 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7835 (mmtt) REVERT: C 69 LYS cc_start: 0.8362 (mttt) cc_final: 0.8116 (mttm) REVERT: C 82 ASP cc_start: 0.8123 (m-30) cc_final: 0.7654 (m-30) REVERT: D 16 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8050 (mt0) REVERT: D 73 ASP cc_start: 0.8158 (t0) cc_final: 0.7858 (t70) REVERT: D 100 TYR cc_start: 0.7881 (t80) cc_final: 0.7400 (t80) REVERT: F 100 TYR cc_start: 0.7442 (t80) cc_final: 0.7101 (t80) REVERT: B 288 ASN cc_start: 0.6996 (t0) cc_final: 0.6474 (p0) REVERT: B 341 PHE cc_start: 0.7027 (m-80) cc_final: 0.6787 (m-80) REVERT: B 407 LEU cc_start: 0.9039 (mt) cc_final: 0.8766 (mt) REVERT: B 451 GLU cc_start: 0.7787 (pt0) cc_final: 0.7455 (pt0) REVERT: B 523 MET cc_start: 0.8741 (ttp) cc_final: 0.8492 (ttt) REVERT: B 585 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 5 outliers final: 4 residues processed: 283 average time/residue: 0.1076 time to fit residues: 43.6925 Evaluate side-chains 215 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 542 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.0243 > 50:) chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 68 ASN A 139 ASN A 222 ASN A 338 ASN A 425 ASN A 436 ASN A 437 GLN A 583 HIS A 590 ASN D 5 GLN F 5 GLN B 155 HIS B 234 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 583 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128451 restraints weight = 16898.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131130 restraints weight = 13070.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131727 restraints weight = 8446.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131754 restraints weight = 6226.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131822 restraints weight = 6084.369| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12681 Z= 0.172 Angle : 0.749 10.927 17192 Z= 0.373 Chirality : 0.047 0.267 1964 Planarity : 0.005 0.052 2133 Dihedral : 6.285 51.495 1716 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.67 % Allowed : 10.15 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.19), residues: 1558 helix: -1.34 (0.19), residues: 630 sheet: -3.17 (0.33), residues: 194 loop : -4.01 (0.18), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 246 TYR 0.018 0.002 TYR D 94 PHE 0.024 0.002 PHE F 79 TRP 0.012 0.001 TRP B 379 HIS 0.025 0.003 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12670) covalent geometry : angle 0.73814 / 0.37 (17166) SS BOND : bond 0.00436 / 0.28 ( 7) SS BOND : angle 0.99728 / 0.65 ( 14) hydrogen bonds : bond 0.04375 / 2.73 ( 444) hydrogen bonds : angle 5.17676 / 3.58 ( 1281) link_BETA1-4 : bond 0.00929 / 0.47 ( 2) link_BETA1-4 : angle 5.98398 / 3.78 ( 6) link_NAG-ASN : bond 0.00457 / 0.24 ( 2) link_NAG-ASN : angle 2.91548 / 1.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 515 MET cc_start: 0.8539 (mmm) cc_final: 0.8258 (mmp) REVERT: A 576 TYR cc_start: 0.9140 (m-80) cc_final: 0.8738 (m-80) REVERT: C 24 LYS cc_start: 0.8259 (ptpp) cc_final: 0.8048 (mmtp) REVERT: E 30 LEU cc_start: 0.9089 (mt) cc_final: 0.8844 (mt) REVERT: B 288 ASN cc_start: 0.7325 (t0) cc_final: 0.7113 (p0) REVERT: B 407 LEU cc_start: 0.9038 (mt) cc_final: 0.8795 (mt) REVERT: B 523 MET cc_start: 0.8325 (ttp) cc_final: 0.7996 (ttt) REVERT: B 585 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7682 (tm-30) outliers start: 36 outliers final: 30 residues processed: 240 average time/residue: 0.0957 time to fit residues: 33.8394 Evaluate side-chains 235 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 109 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS A 582 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124753 restraints weight = 17015.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126134 restraints weight = 13725.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126958 restraints weight = 10362.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127320 restraints weight = 7739.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127394 restraints weight = 7091.913| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12681 Z= 0.216 Angle : 0.727 9.860 17192 Z= 0.367 Chirality : 0.047 0.238 1964 Planarity : 0.004 0.048 2133 Dihedral : 5.990 49.571 1711 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.33 % Allowed : 16.07 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.20), residues: 1558 helix: -0.74 (0.20), residues: 628 sheet: -3.03 (0.34), residues: 190 loop : -3.64 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 246 TYR 0.019 0.002 TYR D 94 PHE 0.033 0.002 PHE F 79 TRP 0.013 0.001 TRP B 379 HIS 0.010 0.002 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (12670) covalent geometry : angle 0.71782 / 0.36 (17166) SS BOND : bond 0.00817 / 0.29 ( 7) SS BOND : angle 1.28965 / 0.83 ( 14) hydrogen bonds : bond 0.04070 / 2.57 ( 444) hydrogen bonds : angle 4.86127 / 3.40 ( 1281) link_BETA1-4 : bond 0.01205 / 0.61 ( 2) link_BETA1-4 : angle 4.94357 / 3.12 ( 6) link_NAG-ASN : bond 0.00217 / 0.11 ( 2) link_NAG-ASN : angle 3.65303 / 2.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6206 (pm20) cc_final: 0.5803 (pm20) REVERT: A 515 MET cc_start: 0.8439 (mmm) cc_final: 0.8190 (mmp) REVERT: A 576 TYR cc_start: 0.9075 (m-80) cc_final: 0.8791 (m-80) REVERT: E 45 ARG cc_start: 0.7390 (ptm160) cc_final: 0.7146 (ttp80) REVERT: F 29 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7998 (pt) REVERT: B 523 MET cc_start: 0.8199 (ttp) cc_final: 0.7902 (ttt) outliers start: 45 outliers final: 34 residues processed: 235 average time/residue: 0.0936 time to fit residues: 32.9687 Evaluate side-chains 225 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.0030 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 243 HIS A 244 GLN A 391 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130817 restraints weight = 16686.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130883 restraints weight = 15227.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132099 restraints weight = 12464.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132797 restraints weight = 9293.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133328 restraints weight = 8385.990| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12681 Z= 0.130 Angle : 0.644 9.190 17192 Z= 0.320 Chirality : 0.044 0.238 1964 Planarity : 0.004 0.045 2133 Dihedral : 5.563 54.626 1710 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.19 % Allowed : 18.59 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.20), residues: 1558 helix: -0.26 (0.21), residues: 628 sheet: -3.01 (0.37), residues: 158 loop : -3.34 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.015 0.001 TYR D 94 PHE 0.018 0.001 PHE F 79 TRP 0.011 0.001 TRP F 35 HIS 0.009 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12670) covalent geometry : angle 0.63552 / 0.32 (17166) SS BOND : bond 0.00366 / 0.17 ( 7) SS BOND : angle 0.82869 / 0.53 ( 14) hydrogen bonds : bond 0.03396 / 2.18 ( 444) hydrogen bonds : angle 4.50032 / 3.14 ( 1281) link_BETA1-4 : bond 0.01308 / 0.66 ( 2) link_BETA1-4 : angle 4.31161 / 2.71 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 3.77940 / 2.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.469 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 78 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8069 (mm) REVERT: A 156 GLU cc_start: 0.6134 (pm20) cc_final: 0.5643 (pm20) REVERT: A 206 ILE cc_start: 0.8766 (mm) cc_final: 0.8323 (mt) REVERT: A 515 MET cc_start: 0.8398 (mmm) cc_final: 0.8177 (mmp) REVERT: A 576 TYR cc_start: 0.9066 (m-80) cc_final: 0.8815 (m-80) REVERT: E 45 ARG cc_start: 0.7366 (ptm160) cc_final: 0.7086 (ttp80) REVERT: B 515 MET cc_start: 0.8079 (mmt) cc_final: 0.7755 (mmm) REVERT: B 523 MET cc_start: 0.8141 (ttp) cc_final: 0.7838 (ttt) outliers start: 43 outliers final: 33 residues processed: 239 average time/residue: 0.0937 time to fit residues: 33.7573 Evaluate side-chains 221 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 139 optimal weight: 0.5980 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130179 restraints weight = 16834.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130796 restraints weight = 13783.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132276 restraints weight = 10691.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132534 restraints weight = 7512.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132754 restraints weight = 6755.143| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12681 Z= 0.132 Angle : 0.634 8.478 17192 Z= 0.313 Chirality : 0.043 0.229 1964 Planarity : 0.004 0.044 2133 Dihedral : 5.424 59.359 1710 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.93 % Allowed : 19.70 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.21), residues: 1558 helix: -0.01 (0.21), residues: 632 sheet: -2.71 (0.37), residues: 168 loop : -3.15 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.015 0.001 TYR D 94 PHE 0.022 0.001 PHE B 578 TRP 0.012 0.001 TRP E 96 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12670) covalent geometry : angle 0.62516 / 0.31 (17166) SS BOND : bond 0.00286 / 0.16 ( 7) SS BOND : angle 0.88019 / 0.55 ( 14) hydrogen bonds : bond 0.03312 / 2.12 ( 444) hydrogen bonds : angle 4.32426 / 3.03 ( 1281) link_BETA1-4 : bond 0.01224 / 0.61 ( 2) link_BETA1-4 : angle 4.29228 / 2.70 ( 6) link_NAG-ASN : bond 0.00098 / 0.05 ( 2) link_NAG-ASN : angle 3.81850 / 2.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.467 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.4712 (OUTLIER) cc_final: 0.4455 (mmt180) REVERT: A 206 ILE cc_start: 0.8710 (mm) cc_final: 0.8322 (mt) REVERT: A 218 SER cc_start: 0.6318 (OUTLIER) cc_final: 0.6093 (p) REVERT: A 247 TYR cc_start: 0.6953 (t80) cc_final: 0.6738 (t80) REVERT: A 515 MET cc_start: 0.8368 (mmm) cc_final: 0.8139 (mmp) REVERT: A 576 TYR cc_start: 0.9063 (m-80) cc_final: 0.8819 (m-80) REVERT: E 45 ARG cc_start: 0.7376 (ptm160) cc_final: 0.7126 (ttp80) REVERT: B 256 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 523 MET cc_start: 0.8113 (ttp) cc_final: 0.7790 (ttt) outliers start: 53 outliers final: 38 residues processed: 239 average time/residue: 0.0923 time to fit residues: 32.9896 Evaluate side-chains 232 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 0.0050 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 0.0020 chunk 26 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 overall best weight: 2.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.171350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141190 restraints weight = 17019.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144709 restraints weight = 8468.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146892 restraints weight = 5262.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148270 restraints weight = 3819.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149030 restraints weight = 3083.148| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12681 Z= 0.196 Angle : 0.680 9.279 17192 Z= 0.341 Chirality : 0.045 0.228 1964 Planarity : 0.004 0.050 2133 Dihedral : 5.555 53.295 1710 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 4.74 % Allowed : 19.70 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.21), residues: 1558 helix: 0.06 (0.21), residues: 620 sheet: -2.72 (0.37), residues: 168 loop : -3.15 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.018 0.002 TYR D 94 PHE 0.027 0.002 PHE F 79 TRP 0.016 0.001 TRP E 96 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (12670) covalent geometry : angle 0.67167 / 0.34 (17166) SS BOND : bond 0.00317 / 0.18 ( 7) SS BOND : angle 1.52806 / 0.94 ( 14) hydrogen bonds : bond 0.03579 / 2.29 ( 444) hydrogen bonds : angle 4.38475 / 3.09 ( 1281) link_BETA1-4 : bond 0.01344 / 0.68 ( 2) link_BETA1-4 : angle 4.07295 / 2.56 ( 6) link_NAG-ASN : bond 0.00094 / 0.05 ( 2) link_NAG-ASN : angle 3.60994 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6325 (pm20) cc_final: 0.5488 (pm20) REVERT: A 218 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6509 (p) REVERT: A 247 TYR cc_start: 0.7166 (t80) cc_final: 0.6846 (t80) REVERT: A 515 MET cc_start: 0.8640 (mmm) cc_final: 0.8365 (mmp) REVERT: A 576 TYR cc_start: 0.9194 (m-80) cc_final: 0.8929 (m-80) REVERT: E 45 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7175 (ttp80) REVERT: F 29 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7968 (pt) REVERT: B 515 MET cc_start: 0.8304 (mmt) cc_final: 0.7749 (mmm) REVERT: B 523 MET cc_start: 0.8366 (ttp) cc_final: 0.8072 (ttt) outliers start: 64 outliers final: 53 residues processed: 247 average time/residue: 0.0899 time to fit residues: 33.4880 Evaluate side-chains 247 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 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 = 0.4119 r_free = 0.4119 target = 0.173396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143599 restraints weight = 17043.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147193 restraints weight = 8372.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149397 restraints weight = 5157.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150884 restraints weight = 3714.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151677 restraints weight = 2945.822| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12681 Z= 0.151 Angle : 0.647 10.360 17192 Z= 0.319 Chirality : 0.044 0.229 1964 Planarity : 0.004 0.045 2133 Dihedral : 5.356 49.221 1710 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.07 % Allowed : 22.30 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1558 helix: 0.20 (0.21), residues: 620 sheet: -2.64 (0.38), residues: 168 loop : -3.01 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.015 0.001 TYR D 94 PHE 0.030 0.002 PHE A 266 TRP 0.015 0.001 TRP E 96 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12670) covalent geometry : angle 0.63814 / 0.32 (17166) SS BOND : bond 0.00281 / 0.15 ( 7) SS BOND : angle 1.08808 / 0.68 ( 14) hydrogen bonds : bond 0.03328 / 2.14 ( 444) hydrogen bonds : angle 4.33860 / 3.05 ( 1281) link_BETA1-4 : bond 0.01254 / 0.63 ( 2) link_BETA1-4 : angle 4.06555 / 2.55 ( 6) link_NAG-ASN : bond 0.00035 / 0.02 ( 2) link_NAG-ASN : angle 3.66482 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.447 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 127 ASP cc_start: 0.7292 (p0) cc_final: 0.6990 (p0) REVERT: A 156 GLU cc_start: 0.6302 (pm20) cc_final: 0.5855 (pm20) REVERT: A 218 SER cc_start: 0.6933 (OUTLIER) cc_final: 0.6683 (p) REVERT: A 247 TYR cc_start: 0.7182 (t80) cc_final: 0.6883 (t80) REVERT: A 515 MET cc_start: 0.8602 (mmm) cc_final: 0.8345 (mmp) REVERT: A 576 TYR cc_start: 0.9186 (m-80) cc_final: 0.8931 (m-80) REVERT: E 45 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7169 (ttp80) REVERT: F 29 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7891 (pt) REVERT: B 256 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 515 MET cc_start: 0.8279 (mmt) cc_final: 0.7835 (mmm) REVERT: B 523 MET cc_start: 0.8331 (ttp) cc_final: 0.7992 (ttt) outliers start: 55 outliers final: 43 residues processed: 238 average time/residue: 0.0948 time to fit residues: 34.3941 Evaluate side-chains 236 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 0.0270 chunk 39 optimal weight: 0.0970 chunk 109 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 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 = 0.4171 r_free = 0.4171 target = 0.179837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152652 restraints weight = 17295.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154811 restraints weight = 9225.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155427 restraints weight = 6100.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156161 restraints weight = 4772.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156101 restraints weight = 4308.982| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12681 Z= 0.111 Angle : 0.608 8.496 17192 Z= 0.298 Chirality : 0.042 0.233 1964 Planarity : 0.004 0.050 2133 Dihedral : 5.036 48.239 1710 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.89 % Allowed : 23.41 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.21), residues: 1558 helix: 0.27 (0.21), residues: 634 sheet: -2.90 (0.36), residues: 170 loop : -2.77 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.011 0.001 TYR B 247 PHE 0.014 0.001 PHE A 208 TRP 0.015 0.001 TRP F 35 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12670) covalent geometry : angle 0.60016 / 0.30 (17166) SS BOND : bond 0.00230 / 0.13 ( 7) SS BOND : angle 0.81721 / 0.51 ( 14) hydrogen bonds : bond 0.03039 / 1.94 ( 444) hydrogen bonds : angle 4.20862 / 2.95 ( 1281) link_BETA1-4 : bond 0.01333 / 0.66 ( 2) link_BETA1-4 : angle 3.85302 / 2.42 ( 6) link_NAG-ASN : bond 0.00096 / 0.05 ( 2) link_NAG-ASN : angle 3.65341 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 127 ASP cc_start: 0.7151 (p0) cc_final: 0.6875 (p0) REVERT: A 156 GLU cc_start: 0.6272 (pm20) cc_final: 0.5810 (pm20) REVERT: A 218 SER cc_start: 0.6905 (OUTLIER) cc_final: 0.6664 (p) REVERT: A 247 TYR cc_start: 0.7066 (t80) cc_final: 0.6843 (t80) REVERT: A 515 MET cc_start: 0.8524 (mmm) cc_final: 0.8270 (mmp) REVERT: A 576 TYR cc_start: 0.9146 (m-80) cc_final: 0.8904 (m-80) REVERT: E 45 ARG cc_start: 0.7398 (ptm160) cc_final: 0.7128 (ttp80) REVERT: B 71 MET cc_start: 0.7104 (mmm) cc_final: 0.6838 (mmm) REVERT: B 515 MET cc_start: 0.8188 (mmt) cc_final: 0.7830 (mmm) REVERT: B 523 MET cc_start: 0.8245 (ttp) cc_final: 0.7907 (ttt) outliers start: 39 outliers final: 30 residues processed: 237 average time/residue: 0.0903 time to fit residues: 32.3882 Evaluate side-chains 227 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 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 = 0.4144 r_free = 0.4144 target = 0.175659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146113 restraints weight = 17064.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149663 restraints weight = 8314.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151912 restraints weight = 5151.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153289 restraints weight = 3710.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154046 restraints weight = 2973.074| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12681 Z= 0.139 Angle : 0.632 9.327 17192 Z= 0.311 Chirality : 0.043 0.227 1964 Planarity : 0.004 0.067 2133 Dihedral : 5.027 49.107 1710 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.11 % Allowed : 23.56 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1558 helix: 0.49 (0.21), residues: 612 sheet: -2.58 (0.37), residues: 180 loop : -2.79 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.028 0.001 TYR A 463 PHE 0.022 0.001 PHE B 578 TRP 0.015 0.001 TRP E 96 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12670) covalent geometry : angle 0.62479 / 0.31 (17166) SS BOND : bond 0.00268 / 0.15 ( 7) SS BOND : angle 0.90060 / 0.59 ( 14) hydrogen bonds : bond 0.03281 / 2.09 ( 444) hydrogen bonds : angle 4.21101 / 2.95 ( 1281) link_BETA1-4 : bond 0.01251 / 0.63 ( 2) link_BETA1-4 : angle 3.66111 / 2.30 ( 6) link_NAG-ASN : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : angle 3.63082 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.361 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 127 ASP cc_start: 0.7195 (p0) cc_final: 0.6936 (p0) REVERT: A 156 GLU cc_start: 0.6287 (pm20) cc_final: 0.5793 (pm20) REVERT: A 218 SER cc_start: 0.7113 (OUTLIER) cc_final: 0.6892 (p) REVERT: A 247 TYR cc_start: 0.7135 (t80) cc_final: 0.6889 (t80) REVERT: A 515 MET cc_start: 0.8549 (mmm) cc_final: 0.8263 (mmp) REVERT: E 45 ARG cc_start: 0.7421 (ptm160) cc_final: 0.7163 (ttp80) REVERT: F 29 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (pt) REVERT: B 71 MET cc_start: 0.7117 (mmm) cc_final: 0.6821 (mmm) REVERT: B 515 MET cc_start: 0.8237 (mmt) cc_final: 0.7864 (mmm) REVERT: B 523 MET cc_start: 0.8255 (ttp) cc_final: 0.7929 (ttt) outliers start: 42 outliers final: 35 residues processed: 225 average time/residue: 0.0888 time to fit residues: 30.3951 Evaluate side-chains 221 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146842 restraints weight = 17002.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148495 restraints weight = 8875.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149632 restraints weight = 5982.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151494 restraints weight = 4694.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151443 restraints weight = 4174.772| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12681 Z= 0.144 Angle : 0.637 8.939 17192 Z= 0.314 Chirality : 0.043 0.229 1964 Planarity : 0.004 0.064 2133 Dihedral : 5.055 49.183 1710 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.19 % Allowed : 23.70 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1558 helix: 0.54 (0.21), residues: 612 sheet: -2.49 (0.37), residues: 180 loop : -2.77 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.019 0.001 TYR A 463 PHE 0.019 0.001 PHE B 578 TRP 0.020 0.001 TRP E 96 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (12670) covalent geometry : angle 0.62998 / 0.31 (17166) SS BOND : bond 0.00266 / 0.15 ( 7) SS BOND : angle 0.84676 / 0.56 ( 14) hydrogen bonds : bond 0.03263 / 2.09 ( 444) hydrogen bonds : angle 4.17757 / 2.93 ( 1281) link_BETA1-4 : bond 0.01321 / 0.67 ( 2) link_BETA1-4 : angle 3.60247 / 2.27 ( 6) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 3.50175 / 2.18 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.470 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 127 ASP cc_start: 0.7257 (p0) cc_final: 0.6980 (p0) REVERT: A 218 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.7118 (p) REVERT: A 233 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8376 (ptpp) REVERT: A 247 TYR cc_start: 0.7164 (t80) cc_final: 0.6766 (t80) REVERT: A 515 MET cc_start: 0.8512 (mmm) cc_final: 0.8240 (mmp) REVERT: A 576 TYR cc_start: 0.9130 (m-80) cc_final: 0.8884 (m-80) REVERT: E 45 ARG cc_start: 0.7435 (ptm160) cc_final: 0.7165 (ttp80) REVERT: F 29 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7826 (pt) REVERT: B 256 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 515 MET cc_start: 0.8224 (mmt) cc_final: 0.7869 (mmm) REVERT: B 523 MET cc_start: 0.8251 (ttp) cc_final: 0.7927 (ttt) outliers start: 43 outliers final: 36 residues processed: 223 average time/residue: 0.0955 time to fit residues: 32.5567 Evaluate side-chains 232 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139911 restraints weight = 16524.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143334 restraints weight = 8226.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145456 restraints weight = 5128.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146721 restraints weight = 3724.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147511 restraints weight = 3042.605| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12681 Z= 0.232 Angle : 0.721 14.030 17192 Z= 0.357 Chirality : 0.046 0.225 1964 Planarity : 0.004 0.058 2133 Dihedral : 5.370 48.654 1710 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.48 % Allowed : 23.56 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.21), residues: 1558 helix: 0.38 (0.21), residues: 612 sheet: -2.58 (0.37), residues: 180 loop : -2.84 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.021 0.002 TYR A 463 PHE 0.026 0.002 PHE F 79 TRP 0.023 0.002 TRP E 96 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (12670) covalent geometry : angle 0.71510 / 0.36 (17166) SS BOND : bond 0.00387 / 0.22 ( 7) SS BOND : angle 1.11809 / 0.75 ( 14) hydrogen bonds : bond 0.03673 / 2.36 ( 444) hydrogen bonds : angle 4.35383 / 3.08 ( 1281) link_BETA1-4 : bond 0.01204 / 0.60 ( 2) link_BETA1-4 : angle 3.52671 / 2.21 ( 6) link_NAG-ASN : bond 0.00048 / 0.02 ( 2) link_NAG-ASN : angle 3.50712 / 2.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.13 seconds wall clock time: 37 minutes 9.85 seconds (2229.85 seconds total)