Starting phenix.real_space_refine on Wed Jun 11 06:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_12300.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_12300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_12300.map" model { file = "/net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_12300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nfd_12300/06_2025/7nfd_12300.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 8.35, per 1000 atoms: 0.67 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: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 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: 1.09 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: 3.27 Time building geometry restraints manager: 3.95 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 - 21.68: 6896 21.68 - 43.35: 513 43.35 - 65.03: 50 65.03 - 86.71: 29 86.71 - 108.38: 11 Dihedral angle restraints: 7499 sinusoidal: 2963 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 7496 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.710 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 16.114 108.383 4582 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP E 92 HIS 0.006 0.002 HIS A 267 PHE 0.035 0.003 PHE B 432 TYR 0.019 0.002 TYR E 91 ARG 0.014 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 2) link_NAG-ASN : angle 4.00821 ( 6) link_BETA1-4 : bond 0.06574 ( 2) link_BETA1-4 : angle 46.07313 ( 6) hydrogen bonds : bond 0.16545 ( 444) hydrogen bonds : angle 7.17437 ( 1281) SS BOND : bond 0.01050 ( 7) SS BOND : angle 2.78388 ( 14) covalent geometry : bond 0.00923 (12670) covalent geometry : angle 1.01630 (17166) *********************** 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 : 1.371 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: 0.7653 (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: 0.2630 time to fit residues: 104.7376 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 : 1.417 ------------------------------------------------------------------------------- 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 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN A 222 ASN A 338 ASN A 424 GLN A 425 ASN A 436 ASN A 437 GLN A 582 GLN A 583 HIS D 5 GLN F 5 GLN B 155 HIS B 234 GLN B 244 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 583 HIS B 617 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133631 restraints weight = 16641.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133586 restraints weight = 13345.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134888 restraints weight = 11899.267| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12681 Z= 0.136 Angle : 0.722 10.778 17192 Z= 0.357 Chirality : 0.045 0.169 1964 Planarity : 0.005 0.049 2133 Dihedral : 9.864 76.490 1800 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.07 % Allowed : 10.44 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.19), residues: 1558 helix: -1.22 (0.19), residues: 630 sheet: -3.19 (0.36), residues: 154 loop : -3.91 (0.18), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.022 0.002 HIS B 243 PHE 0.020 0.002 PHE B 578 TYR 0.018 0.002 TYR A 287 ARG 0.008 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 2) link_NAG-ASN : angle 2.71352 ( 6) link_BETA1-4 : bond 0.01234 ( 2) link_BETA1-4 : angle 7.06651 ( 6) hydrogen bonds : bond 0.04051 ( 444) hydrogen bonds : angle 5.01832 ( 1281) SS BOND : bond 0.00367 ( 7) SS BOND : angle 0.89682 ( 14) covalent geometry : bond 0.00295 (12670) covalent geometry : angle 0.70789 (17166) *********************** 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 274 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.240 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 206 ILE cc_start: 0.8768 (mm) cc_final: 0.8365 (mt) REVERT: A 351 GLN cc_start: 0.5661 (tm-30) cc_final: 0.5393 (tm-30) REVERT: A 515 MET cc_start: 0.8331 (mmm) cc_final: 0.8064 (mmp) REVERT: A 576 TYR cc_start: 0.9034 (m-80) cc_final: 0.8709 (m-80) REVERT: E 30 LEU cc_start: 0.8969 (mt) cc_final: 0.8735 (mt) REVERT: B 407 LEU cc_start: 0.8933 (mt) cc_final: 0.8693 (mt) REVERT: B 523 MET cc_start: 0.8163 (ttp) cc_final: 0.7841 (ttt) outliers start: 28 outliers final: 23 residues processed: 257 average time/residue: 0.2342 time to fit residues: 87.0496 Evaluate side-chains 234 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 D residue 18 LEU 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 E residue 102 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 264 LEU 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 550 ILE Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 121 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 457 HIS ** E 6 GLN ** 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129001 restraints weight = 16842.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131136 restraints weight = 12849.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131887 restraints weight = 9021.413| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12681 Z= 0.156 Angle : 0.663 8.586 17192 Z= 0.335 Chirality : 0.044 0.170 1964 Planarity : 0.004 0.045 2133 Dihedral : 6.908 47.130 1795 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.04 % Allowed : 15.04 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.20), residues: 1558 helix: -0.71 (0.20), residues: 634 sheet: -3.08 (0.35), residues: 180 loop : -3.63 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.009 0.002 HIS B 243 PHE 0.026 0.002 PHE F 79 TYR 0.018 0.001 TYR D 94 ARG 0.005 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 2.79144 ( 6) link_BETA1-4 : bond 0.00926 ( 2) link_BETA1-4 : angle 2.90045 ( 6) hydrogen bonds : bond 0.03746 ( 444) hydrogen bonds : angle 4.69545 ( 1281) SS BOND : bond 0.00359 ( 7) SS BOND : angle 1.55288 ( 14) covalent geometry : bond 0.00357 (12670) covalent geometry : angle 0.65797 (17166) *********************** 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 260 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.409 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 156 GLU cc_start: 0.5987 (pm20) cc_final: 0.5552 (pm20) REVERT: A 206 ILE cc_start: 0.8786 (mm) cc_final: 0.8418 (mt) REVERT: A 576 TYR cc_start: 0.9081 (m-80) cc_final: 0.8796 (m-80) REVERT: E 30 LEU cc_start: 0.9060 (mt) cc_final: 0.8846 (mt) REVERT: B 523 MET cc_start: 0.8160 (ttp) cc_final: 0.7818 (ttt) outliers start: 41 outliers final: 30 residues processed: 241 average time/residue: 0.2284 time to fit residues: 82.7366 Evaluate side-chains 229 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain C residue 85 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 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 486 SER 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 143 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 0.0010 chunk 62 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132018 restraints weight = 16706.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132950 restraints weight = 15629.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133665 restraints weight = 12231.316| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2822 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= 0.129 Angle : 0.618 9.209 17192 Z= 0.312 Chirality : 0.043 0.209 1964 Planarity : 0.004 0.043 2133 Dihedral : 6.114 48.720 1794 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.59 % Allowed : 17.56 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1558 helix: -0.30 (0.20), residues: 638 sheet: -3.02 (0.34), residues: 192 loop : -3.37 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.007 0.001 HIS B 267 PHE 0.020 0.001 PHE F 79 TYR 0.015 0.001 TYR D 94 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 2) link_NAG-ASN : angle 2.21891 ( 6) link_BETA1-4 : bond 0.00654 ( 2) link_BETA1-4 : angle 3.05831 ( 6) hydrogen bonds : bond 0.03396 ( 444) hydrogen bonds : angle 4.46093 ( 1281) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.27356 ( 14) covalent geometry : bond 0.00292 (12670) covalent geometry : angle 0.61297 (17166) *********************** 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 243 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 1.414 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 206 ILE cc_start: 0.8705 (mm) cc_final: 0.8340 (mt) REVERT: A 293 PHE cc_start: 0.7041 (t80) cc_final: 0.6813 (t80) REVERT: A 576 TYR cc_start: 0.9057 (m-80) cc_final: 0.8823 (m-80) REVERT: B 515 MET cc_start: 0.8052 (mmt) cc_final: 0.7778 (mmm) REVERT: B 523 MET cc_start: 0.8100 (ttp) cc_final: 0.7799 (ttt) outliers start: 35 outliers final: 27 residues processed: 226 average time/residue: 0.2104 time to fit residues: 72.2152 Evaluate side-chains 218 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 391 ASN 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 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 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 69 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 264 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN E 6 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129319 restraints weight = 16711.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129274 restraints weight = 16733.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130520 restraints weight = 13943.437| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3017 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= 0.160 Angle : 0.635 10.363 17192 Z= 0.319 Chirality : 0.043 0.164 1964 Planarity : 0.004 0.042 2133 Dihedral : 5.966 54.213 1794 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.56 % Allowed : 18.44 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 1558 helix: -0.10 (0.21), residues: 632 sheet: -2.92 (0.35), residues: 180 loop : -3.11 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS B 267 PHE 0.024 0.001 PHE F 79 TYR 0.023 0.001 TYR A 463 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 2.19456 ( 6) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 2.78477 ( 6) hydrogen bonds : bond 0.03462 ( 444) hydrogen bonds : angle 4.39852 ( 1281) SS BOND : bond 0.00410 ( 7) SS BOND : angle 0.98290 ( 14) covalent geometry : bond 0.00370 (12670) covalent geometry : angle 0.63121 (17166) *********************** 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 248 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 1.393 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6162 (pm20) cc_final: 0.5818 (pm20) REVERT: A 218 SER cc_start: 0.6217 (OUTLIER) cc_final: 0.5991 (p) REVERT: A 576 TYR cc_start: 0.9058 (m-80) cc_final: 0.8833 (m-80) REVERT: E 45 ARG cc_start: 0.7394 (ptm160) cc_final: 0.7124 (ttp80) REVERT: F 29 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7904 (pt) REVERT: B 523 MET cc_start: 0.8103 (ttp) cc_final: 0.7753 (ttt) outliers start: 48 outliers final: 39 residues processed: 230 average time/residue: 0.2224 time to fit residues: 76.2587 Evaluate side-chains 229 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 168 LEU 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 510 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU 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 25 THR 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 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 69 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 398 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129998 restraints weight = 16999.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129710 restraints weight = 17015.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130967 restraints weight = 14052.051| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3253 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= 0.157 Angle : 0.624 8.716 17192 Z= 0.316 Chirality : 0.043 0.164 1964 Planarity : 0.004 0.041 2133 Dihedral : 5.847 59.806 1794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.22 % Allowed : 19.19 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.21), residues: 1558 helix: 0.05 (0.21), residues: 626 sheet: -2.66 (0.37), residues: 168 loop : -3.03 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 96 HIS 0.008 0.001 HIS B 267 PHE 0.023 0.001 PHE F 79 TYR 0.017 0.001 TYR A 463 ARG 0.003 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 2) link_NAG-ASN : angle 1.98853 ( 6) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 2.52448 ( 6) hydrogen bonds : bond 0.03372 ( 444) hydrogen bonds : angle 4.32810 ( 1281) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.15431 ( 14) covalent geometry : bond 0.00365 (12670) covalent geometry : angle 0.62119 (17166) *********************** 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 259 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 156 GLU cc_start: 0.6157 (pm20) cc_final: 0.5727 (pm20) REVERT: A 218 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6253 (p) REVERT: E 45 ARG cc_start: 0.7390 (ptm160) cc_final: 0.7125 (ttp80) REVERT: F 29 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7846 (pt) REVERT: B 523 MET cc_start: 0.8111 (ttp) cc_final: 0.7774 (ttt) outliers start: 57 outliers final: 45 residues processed: 238 average time/residue: 0.2191 time to fit residues: 78.2844 Evaluate side-chains 237 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 168 LEU 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 489 PHE Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 638 VAL 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 80 PHE 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 65 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 69 SER 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 135 THR 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 399 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 550 ILE 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 142 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144210 restraints weight = 17371.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146611 restraints weight = 9985.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147269 restraints weight = 7722.802| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12681 Z= 0.210 Angle : 0.685 9.670 17192 Z= 0.348 Chirality : 0.045 0.167 1964 Planarity : 0.004 0.040 2133 Dihedral : 5.976 50.299 1794 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 5.19 % Allowed : 19.70 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.21), residues: 1558 helix: -0.02 (0.21), residues: 626 sheet: -2.69 (0.37), residues: 168 loop : -3.07 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 96 HIS 0.015 0.002 HIS A 267 PHE 0.030 0.002 PHE F 79 TYR 0.018 0.002 TYR D 94 ARG 0.006 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 2) link_NAG-ASN : angle 2.04410 ( 6) link_BETA1-4 : bond 0.00346 ( 2) link_BETA1-4 : angle 2.48980 ( 6) hydrogen bonds : bond 0.03750 ( 444) hydrogen bonds : angle 4.43159 ( 1281) SS BOND : bond 0.00331 ( 7) SS BOND : angle 1.79994 ( 14) covalent geometry : bond 0.00490 (12670) covalent geometry : angle 0.68119 (17166) *********************** 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 277 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 1.388 Fit side-chains REVERT: A 184 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.4771 (mmt180) REVERT: E 45 ARG cc_start: 0.7428 (ptm160) cc_final: 0.7158 (ttp80) REVERT: F 29 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7961 (pt) REVERT: B 523 MET cc_start: 0.8353 (ttp) cc_final: 0.8007 (ttt) outliers start: 70 outliers final: 55 residues processed: 252 average time/residue: 0.2048 time to fit residues: 77.7099 Evaluate side-chains 248 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 184 ARG 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 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 638 VAL 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 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 25 THR 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 65 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 F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 39 PHE 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 225 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 456 ILE 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 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** 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 244 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.172425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144006 restraints weight = 17183.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145326 restraints weight = 9513.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146591 restraints weight = 6610.311| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12681 Z= 0.165 Angle : 0.645 9.511 17192 Z= 0.325 Chirality : 0.043 0.163 1964 Planarity : 0.004 0.052 2133 Dihedral : 5.752 47.033 1794 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.44 % Allowed : 21.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.21), residues: 1558 helix: 0.08 (0.21), residues: 620 sheet: -2.58 (0.38), residues: 168 loop : -2.96 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 96 HIS 0.006 0.001 HIS A 267 PHE 0.044 0.002 PHE A 266 TYR 0.015 0.001 TYR D 94 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 1.92804 ( 6) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 2.44573 ( 6) hydrogen bonds : bond 0.03467 ( 444) hydrogen bonds : angle 4.34714 ( 1281) SS BOND : bond 0.00288 ( 7) SS BOND : angle 1.37956 ( 14) covalent geometry : bond 0.00385 (12670) covalent geometry : angle 0.64194 (17166) *********************** 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 269 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 1.313 Fit side-chains TARDY: cannot create tardy model for: "THR F 93 " (corrupted residue). Skipping it. REVERT: A 156 GLU cc_start: 0.6318 (pm20) cc_final: 0.5945 (pm20) REVERT: A 159 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5832 (tm-30) REVERT: A 184 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.4926 (mmt180) REVERT: A 387 ASN cc_start: 0.7788 (t0) cc_final: 0.7577 (t0) REVERT: E 45 ARG cc_start: 0.7455 (ptm160) cc_final: 0.7202 (ttp80) REVERT: F 29 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7887 (pt) REVERT: B 256 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7801 (pt) REVERT: B 523 MET cc_start: 0.8319 (ttp) cc_final: 0.8001 (ttt) outliers start: 60 outliers final: 50 residues processed: 246 average time/residue: 0.2183 time to fit residues: 82.0693 Evaluate side-chains 251 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 184 ARG 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 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 638 VAL 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 25 THR 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 65 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 F residue 29 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain B residue 88 SER 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 225 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 456 ILE 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 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** 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 = 0.4158 r_free = 0.4158 target = 0.177057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148789 restraints weight = 17048.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150744 restraints weight = 8968.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151882 restraints weight = 6027.072| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3846 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= 0.116 Angle : 0.614 11.587 17192 Z= 0.305 Chirality : 0.042 0.166 1964 Planarity : 0.004 0.047 2133 Dihedral : 5.393 48.000 1794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.81 % Allowed : 23.33 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1558 helix: 0.35 (0.21), residues: 618 sheet: -2.65 (0.40), residues: 150 loop : -2.76 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 35 HIS 0.004 0.001 HIS A 243 PHE 0.035 0.001 PHE A 266 TYR 0.011 0.001 TYR D 94 ARG 0.003 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 2) link_NAG-ASN : angle 1.82143 ( 6) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 2.32189 ( 6) hydrogen bonds : bond 0.03127 ( 444) hydrogen bonds : angle 4.21805 ( 1281) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.09737 ( 14) covalent geometry : bond 0.00261 (12670) covalent geometry : angle 0.61074 (17166) *********************** 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 252 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.225 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: 0.7291 (p0) cc_final: 0.7019 (p0) REVERT: A 156 GLU cc_start: 0.6232 (pm20) cc_final: 0.5873 (pm20) REVERT: A 184 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.4888 (mmt180) REVERT: A 293 PHE cc_start: 0.6910 (t80) cc_final: 0.6421 (t80) REVERT: A 294 PHE cc_start: 0.8034 (m-80) cc_final: 0.7762 (m-80) REVERT: E 45 ARG cc_start: 0.7428 (ptm160) cc_final: 0.7168 (ttp80) REVERT: B 256 LEU cc_start: 0.8347 (pt) cc_final: 0.8122 (mp) REVERT: B 515 MET cc_start: 0.8191 (mmt) cc_final: 0.7705 (mmm) REVERT: B 523 MET cc_start: 0.8294 (ttp) cc_final: 0.7908 (ttt) outliers start: 38 outliers final: 31 residues processed: 235 average time/residue: 0.2262 time to fit residues: 78.2460 Evaluate side-chains 222 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 608 CYS 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 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 73 LEU Chi-restraints excluded: chain E residue 82 ASP 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 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 550 ILE Chi-restraints excluded: chain B residue 608 CYS 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 115 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.168770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140830 restraints weight = 17145.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143801 restraints weight = 8880.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144361 restraints weight = 5051.870| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12681 Z= 0.264 Angle : 0.742 12.720 17192 Z= 0.374 Chirality : 0.047 0.183 1964 Planarity : 0.005 0.099 2133 Dihedral : 5.888 48.385 1794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.26 % Allowed : 23.33 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1558 helix: 0.06 (0.21), residues: 618 sheet: -2.53 (0.38), residues: 168 loop : -2.85 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 96 HIS 0.006 0.001 HIS A 243 PHE 0.041 0.002 PHE A 266 TYR 0.020 0.002 TYR D 94 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 1.95473 ( 6) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 2.46132 ( 6) hydrogen bonds : bond 0.03840 ( 444) hydrogen bonds : angle 4.44067 ( 1281) SS BOND : bond 0.00453 ( 7) SS BOND : angle 1.51665 ( 14) covalent geometry : bond 0.00617 (12670) covalent geometry : angle 0.73915 (17166) ********************** 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 242 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.411 Fit side-chains REVERT: A 127 ASP cc_start: 0.7282 (p0) cc_final: 0.7023 (p0) REVERT: A 184 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.5028 (mmt180) REVERT: A 294 PHE cc_start: 0.8142 (m-80) cc_final: 0.7889 (m-80) REVERT: E 45 ARG cc_start: 0.7461 (ptm160) cc_final: 0.7191 (ttp80) REVERT: B 71 MET cc_start: 0.7135 (mmm) cc_final: 0.6877 (mmm) REVERT: B 256 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7880 (pt) REVERT: B 523 MET cc_start: 0.8340 (ttp) cc_final: 0.8024 (ttt) outliers start: 44 outliers final: 41 residues processed: 225 average time/residue: 0.3254 time to fit residues: 111.8134 Evaluate side-chains 237 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 196 ILE 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 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 568 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 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 73 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 82 ASP 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 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 456 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 651 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.343 > 50: distance: 10 - 99: 25.232 distance: 25 - 83: 19.791 distance: 43 - 49: 6.810 distance: 49 - 50: 8.985 distance: 49 - 55: 23.614 distance: 50 - 51: 18.040 distance: 50 - 53: 25.077 distance: 51 - 52: 11.596 distance: 53 - 54: 17.624 distance: 54 - 55: 10.198 distance: 56 - 57: 20.184 distance: 57 - 58: 17.488 distance: 58 - 59: 20.782 distance: 58 - 60: 24.188 distance: 60 - 61: 11.390 distance: 61 - 62: 20.015 distance: 61 - 64: 11.550 distance: 62 - 63: 3.589 distance: 62 - 68: 10.920 distance: 64 - 65: 15.040 distance: 65 - 66: 3.970 distance: 65 - 67: 10.092 distance: 68 - 69: 4.677 distance: 69 - 70: 32.505 distance: 69 - 72: 15.180 distance: 70 - 71: 31.145 distance: 70 - 73: 9.130 distance: 73 - 74: 6.471 distance: 73 - 79: 14.988 distance: 74 - 75: 15.602 distance: 74 - 77: 15.971 distance: 75 - 76: 22.699 distance: 75 - 80: 9.134 distance: 77 - 78: 17.840 distance: 78 - 79: 8.661 distance: 80 - 81: 5.751 distance: 81 - 82: 5.839 distance: 81 - 84: 11.982 distance: 82 - 83: 25.244 distance: 82 - 91: 18.856 distance: 84 - 85: 11.888 distance: 85 - 86: 5.847 distance: 86 - 87: 6.717 distance: 87 - 88: 13.029 distance: 88 - 89: 21.795 distance: 91 - 92: 4.459 distance: 92 - 93: 20.531 distance: 92 - 95: 7.169 distance: 93 - 94: 18.091 distance: 93 - 99: 12.544 distance: 95 - 96: 31.965 distance: 96 - 97: 3.211 distance: 96 - 98: 6.871 distance: 99 - 100: 3.808 distance: 100 - 101: 5.260 distance: 100 - 103: 4.600 distance: 101 - 102: 3.158 distance: 101 - 107: 12.930 distance: 103 - 104: 4.589 distance: 104 - 105: 18.120 distance: 104 - 106: 16.390 distance: 107 - 108: 16.538 distance: 108 - 109: 14.136 distance: 108 - 111: 27.378 distance: 109 - 110: 18.908 distance: 109 - 115: 25.352 distance: 111 - 112: 9.577 distance: 111 - 113: 32.137 distance: 112 - 114: 17.646 distance: 115 - 116: 14.786 distance: 116 - 117: 24.832 distance: 116 - 119: 36.124 distance: 117 - 121: 32.707