Starting phenix.real_space_refine on Fri Jul 3 00:33:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.map" model { file = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2026/7b1d_11984.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 47 5.16 5 C 6913 2.51 5 N 1882 2.21 5 O 2125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10967 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5573 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 33, 'TRANS': 719} Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 589 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 17, 'ASN:plan1': 9, 'PHE:plan': 6, 'ASP:plan': 19, 'ARG:plan': 10, 'HIS:plan': 6, 'GLN:plan1': 13, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 329 Chain: "C" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5226 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1034 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 26, 'ARG:plan': 13, 'HIS:plan': 10, 'GLN:plan1': 22, 'ASN:plan1': 21, 'PHE:plan': 8, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 491 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10967 At special positions: 0 Unit cell: (94.62, 125.33, 191.73, 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 47 16.00 O 2125 8.00 N 1882 7.00 C 6913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 561 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 767 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 783 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN B 481 " " NAG B 801 " - " ASN B 521 " " NAG B 802 " - " ASN B 194 " " NAG B 803 " - " ASN B 634 " " NAG C 801 " - " ASN C 194 " " NAG D 1 " - " ASN B 151 " " NAG E 1 " - " ASN C 481 " " NAG F 1 " - " ASN C 151 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 442.4 milliseconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 18 sheets defined 10.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.105A pdb=" N GLU B 144 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.608A pdb=" N LEU B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.687A pdb=" N VAL B 470 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.542A pdb=" N THR B 675 " --> pdb=" O PRO B 672 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 676 " --> pdb=" O ASN B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 716 through 723 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.179A pdb=" N LEU B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.928A pdb=" N PHE C 143 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 144 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 514 through 516 No H-bonds generated for 'chain 'C' and resid 514 through 516' Processing helix chain 'C' and resid 560 through 562 No H-bonds generated for 'chain 'C' and resid 560 through 562' Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 597 through 601 Processing helix chain 'C' and resid 603 through 607 Processing helix chain 'C' and resid 716 through 721 removed outlier: 3.882A pdb=" N ALA C 721 " --> pdb=" O ASP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.282A pdb=" N SER C 747 " --> pdb=" O CYS C 743 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 748 " --> pdb=" O PRO C 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.100A pdb=" N VAL B 74 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B 102 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 155 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR B 129 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.724A pdb=" N ALA B 92 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N ALA B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY B 94 " --> pdb=" O ALA B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 137 removed outlier: 5.426A pdb=" N ILE B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176 removed outlier: 6.795A pdb=" N LEU B 175 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 198 " --> pdb=" O SER B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 248 removed outlier: 3.523A pdb=" N GLU B 271 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 270 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 319 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 367 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 477 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 501 " --> pdb=" O ASN B 525 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 548 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASN B 581 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 550 " --> pdb=" O ASN B 581 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.597A pdb=" N ARG B 586 " --> pdb=" O LEU B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AA9, first strand: chain 'B' and resid 659 through 662 removed outlier: 6.852A pdb=" N LEU B 659 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 683 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 661 " --> pdb=" O LEU B 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 738 through 739 removed outlier: 3.771A pdb=" N TRP B 739 " --> pdb=" O ARG B 766 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.488A pdb=" N VAL C 74 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL C 102 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 removed outlier: 5.911A pdb=" N ILE C 136 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER C 160 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.645A pdb=" N THR C 273 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 294 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 319 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 343 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 367 " --> pdb=" O TYR C 392 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 415 " --> pdb=" O TYR C 440 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 477 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 510 through 512 removed outlier: 6.855A pdb=" N LEU C 511 " --> pdb=" O LEU C 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 523 through 525 removed outlier: 6.780A pdb=" N ILE C 548 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN C 581 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 550 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 630 through 631 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 684 removed outlier: 6.096A pdb=" N LEU C 683 " --> pdb=" O ASP C 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 128 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3281 1.33 - 1.46: 1698 1.46 - 1.58: 6110 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 11147 Sorted by residual: bond pdb=" N CYS C 561 " pdb=" CA CYS C 561 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.21e-02 6.83e+03 1.50e+01 bond pdb=" N ILE C 705 " pdb=" CA ILE C 705 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C 704 " pdb=" CA ILE C 704 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.17e-02 7.31e+03 9.77e+00 bond pdb=" N ILE C 531 " pdb=" CA ILE C 531 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.11e+00 bond pdb=" C PRO C 590 " pdb=" O PRO C 590 " ideal model delta sigma weight residual 1.243 1.218 0.025 8.50e-03 1.38e+04 8.92e+00 ... (remaining 11142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 14559 1.56 - 3.12: 573 3.12 - 4.68: 90 4.68 - 6.23: 18 6.23 - 7.79: 3 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N CYS C 561 " pdb=" CA CYS C 561 " pdb=" C CYS C 561 " ideal model delta sigma weight residual 111.28 116.68 -5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N PRO C 591 " pdb=" CA PRO C 591 " pdb=" C PRO C 591 " ideal model delta sigma weight residual 113.53 107.03 6.50 1.39e+00 5.18e-01 2.19e+01 angle pdb=" N LYS C 565 " pdb=" CA LYS C 565 " pdb=" C LYS C 565 " ideal model delta sigma weight residual 111.69 106.21 5.48 1.23e+00 6.61e-01 1.98e+01 angle pdb=" CA LEU C 557 " pdb=" C LEU C 557 " pdb=" O LEU C 557 " ideal model delta sigma weight residual 122.27 117.51 4.76 1.16e+00 7.43e-01 1.69e+01 angle pdb=" O LEU C 446 " pdb=" C LEU C 446 " pdb=" N ALA C 447 " ideal model delta sigma weight residual 122.87 118.03 4.84 1.23e+00 6.61e-01 1.55e+01 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6238 17.67 - 35.34: 401 35.34 - 53.01: 72 53.01 - 70.68: 18 70.68 - 88.35: 10 Dihedral angle restraints: 6739 sinusoidal: 2290 harmonic: 4449 Sorted by residual: dihedral pdb=" CB CYS C 741 " pdb=" SG CYS C 741 " pdb=" SG CYS C 767 " pdb=" CB CYS C 767 " ideal model delta sinusoidal sigma weight residual -86.00 -174.35 88.35 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS C 78 " pdb=" SG CYS C 78 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual -86.00 -171.99 85.99 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C 559 " pdb=" SG CYS C 559 " pdb=" SG CYS C 587 " pdb=" CB CYS C 587 " ideal model delta sinusoidal sigma weight residual 93.00 165.32 -72.32 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 6736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1456 0.050 - 0.099: 331 0.099 - 0.149: 87 0.149 - 0.198: 11 0.198 - 0.248: 2 Chirality restraints: 1887 Sorted by residual: chirality pdb=" CB ILE B 548 " pdb=" CA ILE B 548 " pdb=" CG1 ILE B 548 " pdb=" CG2 ILE B 548 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA CYS B 57 " pdb=" N CYS B 57 " pdb=" C CYS B 57 " pdb=" CB CYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 151 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1884 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 446 " -0.039 2.00e-02 2.50e+03 7.56e-02 5.71e+01 pdb=" C LEU C 446 " 0.131 2.00e-02 2.50e+03 pdb=" O LEU C 446 " -0.049 2.00e-02 2.50e+03 pdb=" N ALA C 447 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 671 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO B 672 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 561 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C CYS C 561 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS C 561 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 562 " 0.012 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 11344 3.28 - 3.82: 17340 3.82 - 4.36: 20683 4.36 - 4.90: 35275 Nonbonded interactions: 85351 Sorted by model distance: nonbonded pdb=" O ASN B 506 " pdb=" ND2 ASN B 529 " model vdw 2.197 3.120 nonbonded pdb=" OD1 ASN B 506 " pdb=" ND2 ASN B 529 " model vdw 2.199 3.120 nonbonded pdb=" O ARG C 249 " pdb=" OG1 THR C 273 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU C 207 " pdb=" NE2 GLN C 209 " model vdw 2.256 3.120 nonbonded pdb=" O ASP C 108 " pdb=" OH TYR C 142 " model vdw 2.257 3.040 ... (remaining 85346 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 33 or (resid 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 83 or (resid 84 and (name N or name CA or nam \ e C or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or n \ ame C or name O or name CB )) or resid 87 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 132 or (resid \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throug \ h 162 or (resid 163 through 164 and (name N or name CA or name C or name O or na \ me CB )) or resid 165 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 through 189 or (resid 190 through 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 8 through 229 or (resid 230 and (name N or name CA or name C or name O or name C \ B )) or resid 231 through 256 or (resid 257 through 259 and (name N or name CA o \ r name C or name O or name CB )) or resid 260 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB )) or resid 272 through 406 or (re \ sid 407 and (name N or name CA or name C or name O or name CB )) or resid 408 th \ rough 447 or (resid 448 through 452 and (name N or name CA or name C or name O o \ r name CB )) or resid 453 through 468 or (resid 469 through 473 and (name N or n \ ame CA or name C or name O or name CB )) or resid 474 through 487 or (resid 488 \ through 490 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 1 or (resid 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 539 or (resid 540 through 543 and (name N or name \ CA or name C or name O or name CB )) or resid 544 through 557 or (resid 558 and \ (name N or name CA or name C or name O or name CB )) or resid 559 or (resid 560 \ and (name N or name CA or name C or name O or name CB )) or resid 561 through 56 \ 3 or (resid 564 through 576 and (name N or name CA or name C or name O or name C \ B )) or resid 577 through 580 or (resid 581 and (name N or name CA or name C or \ name O or name CB )) or resid 582 or (resid 583 through 584 and (name N or name \ CA or name C or name O or name CB )) or resid 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 or (resid 588 through 589 \ and (name N or name CA or name C or name O or name CB )) or resid 590 through 59 \ 1 or (resid 592 through 593 and (name N or name CA or name C or name O or name C \ B )) or resid 594 or (resid 595 through 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 600 or (resid 601 through 607 and (nam \ e N or name CA or name C or name O or name CB )) or resid 608 or (resid 609 thro \ ugh 615 and (name N or name CA or name C or name O or name CB )) or resid 616 th \ rough 623 or (resid 624 through 634 and (name N or name CA or name C or name O o \ r name CB )) or resid 635 or (resid 636 and (name N or name CA or name C or name \ O or name CB )) or resid 637 or (resid 638 and (name N or name CA or name C or \ name O or name CB )) or resid 639 through 645 or (resid 646 and (name N or name \ CA or name C or name O or name CB )) or resid 647 or (resid 648 and (name N or n \ ame CA or name C or name O or name CB )) or resid 649 or (resid 650 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 66 \ 8 or (resid 669 through 671 and (name N or name CA or name C or name O or name C \ B )) or resid 672 or (resid 673 through 694 and (name N or name CA or name C or \ name O or name CB )) or resid 695 through 696 or (resid 697 through 698 and (nam \ e N or name CA or name C or name O or name CB )) or resid 699 or (resid 700 thro \ ugh 740 and (name N or name CA or name C or name O or name CB )) or resid 741 th \ rough 777 or (resid 778 through 782 and (name N or name CA or name C or name O o \ r name CB )) or resid 783 through 801)) selection = (chain 'C' and (resid 33 through 36 or (resid 37 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 50 or (resid 51 through \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 59 or (resid 60 through 61 and (name N or name CA or name C or name O or name C \ B )) or resid 62 through 66 or (resid 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 79 or (resid 80 through 81 and (name N or \ name CA or name C or name O or name CB )) or resid 82 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 24 \ 8 or (resid 249 and (name N or name CA or name C or name O or name CB )) or resi \ d 250 through 251 or (resid 252 and (name N or name CA or name C or name O or na \ me CB )) or resid 253 through 272 or (resid 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 354 or (resid 355 through 356 and \ (name N or name CA or name C or name O or name CB )) or resid 357 through 385 or \ (resid 386 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 7 through 454 or (resid 455 through 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 through 489 or (resid 490 and (name N or name CA o \ r name C or name O or name CB )) or resid 491 through 801)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.004 0.047 11177 Z= 0.254 Angle : 0.725 8.670 15315 Z= 0.421 Chirality : 0.047 0.248 1887 Planarity : 0.004 0.076 2005 Dihedral : 12.495 85.658 3771 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.29 % Allowed : 0.48 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1501 helix: -0.12 (0.64), residues: 71 sheet: -1.43 (0.36), residues: 230 loop : -0.99 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.014 0.001 TYR B 138 PHE 0.015 0.001 PHE C 85 TRP 0.002 0.001 TRP B 491 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.25 (11147) covalent geometry : angle 0.70736 / 0.42 (15243) SS BOND : bond 0.00418 / 0.27 ( 18) SS BOND : angle 0.91577 / 0.73 ( 36) hydrogen bonds : bond 0.24968 / 17.48 ( 128) hydrogen bonds : angle 8.46961 / 5.92 ( 279) link_BETA1-4 : bond 0.01291 / 0.66 ( 4) link_BETA1-4 : angle 5.30493 / 3.29 ( 12) link_NAG-ASN : bond 0.00147 / 0.09 ( 8) link_NAG-ASN : angle 1.38028 / 1.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.288 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.0639 time to fit residues: 3.9069 Evaluate side-chains 25 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.062113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.045505 restraints weight = 59210.329| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.45 r_work: 0.3096 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11177 Z= 0.139 Angle : 0.590 7.570 15315 Z= 0.296 Chirality : 0.043 0.170 1887 Planarity : 0.004 0.068 2005 Dihedral : 4.479 27.029 1573 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.38 % Allowed : 3.26 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.21), residues: 1501 helix: 0.20 (0.61), residues: 73 sheet: -1.21 (0.35), residues: 251 loop : -0.90 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.009 0.001 TYR B 56 PHE 0.013 0.001 PHE B 656 TRP 0.002 0.000 TRP C 491 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11147) covalent geometry : angle 0.57570 / 0.29 (15243) SS BOND : bond 0.00248 / 0.15 ( 18) SS BOND : angle 0.80230 / 0.65 ( 36) hydrogen bonds : bond 0.04452 / 3.27 ( 128) hydrogen bonds : angle 6.01704 / 4.25 ( 279) link_BETA1-4 : bond 0.01330 / 0.68 ( 4) link_BETA1-4 : angle 4.27888 / 2.59 ( 12) link_NAG-ASN : bond 0.00177 / 0.12 ( 8) link_NAG-ASN : angle 1.36732 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.415 Fit side-chains REVERT: C 594 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7748 (tp) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.0721 time to fit residues: 4.0339 Evaluate side-chains 27 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 549 ASN B 554 HIS ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN C 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.058962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.042130 restraints weight = 61311.370| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.43 r_work: 0.2987 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.139 11177 Z= 0.464 Angle : 0.899 10.229 15315 Z= 0.429 Chirality : 0.050 0.212 1887 Planarity : 0.005 0.064 2005 Dihedral : 5.720 26.674 1573 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.96 % Allowed : 6.90 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1501 helix: -0.74 (0.52), residues: 85 sheet: -1.71 (0.34), residues: 257 loop : -1.02 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 475 TYR 0.024 0.003 TYR C 440 PHE 0.020 0.002 PHE C 76 TRP 0.009 0.002 TRP C 491 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.46 (11147) covalent geometry : angle 0.88541 / 0.43 (15243) SS BOND : bond 0.00376 / 0.24 ( 18) SS BOND : angle 1.19156 / 0.88 ( 36) hydrogen bonds : bond 0.04637 / 3.35 ( 128) hydrogen bonds : angle 6.60198 / 4.63 ( 279) link_BETA1-4 : bond 0.01252 / 0.65 ( 4) link_BETA1-4 : angle 4.43958 / 2.55 ( 12) link_NAG-ASN : bond 0.00979 / 0.52 ( 8) link_NAG-ASN : angle 2.38189 / 1.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.364 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 31 average time/residue: 0.0658 time to fit residues: 4.1514 Evaluate side-chains 30 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 140 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN C 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.060393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.043732 restraints weight = 60318.916| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.44 r_work: 0.3042 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11177 Z= 0.190 Angle : 0.622 7.909 15315 Z= 0.309 Chirality : 0.044 0.174 1887 Planarity : 0.004 0.056 2005 Dihedral : 5.022 25.603 1573 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.25 % Allowed : 8.24 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.22), residues: 1501 helix: 0.17 (0.58), residues: 79 sheet: -1.60 (0.35), residues: 252 loop : -0.88 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.010 0.001 TYR C 440 PHE 0.014 0.001 PHE B 656 TRP 0.004 0.001 TRP C 491 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (11147) covalent geometry : angle 0.60811 / 0.31 (15243) SS BOND : bond 0.00268 / 0.17 ( 18) SS BOND : angle 0.85295 / 0.71 ( 36) hydrogen bonds : bond 0.03293 / 2.41 ( 128) hydrogen bonds : angle 5.82452 / 4.08 ( 279) link_BETA1-4 : bond 0.01258 / 0.65 ( 4) link_BETA1-4 : angle 4.15357 / 2.47 ( 12) link_NAG-ASN : bond 0.00352 / 0.21 ( 8) link_NAG-ASN : angle 1.48868 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.481 Fit side-chains REVERT: B 411 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8752 (t0) REVERT: B 598 MET cc_start: 0.9191 (mpp) cc_final: 0.8851 (mpp) REVERT: C 441 MET cc_start: 0.9183 (mmm) cc_final: 0.8928 (mmm) outliers start: 13 outliers final: 10 residues processed: 35 average time/residue: 0.0681 time to fit residues: 4.5173 Evaluate side-chains 35 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.059974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.043280 restraints weight = 60138.901| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.35 r_work: 0.3022 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 11177 Z= 0.242 Angle : 0.648 8.289 15315 Z= 0.318 Chirality : 0.044 0.170 1887 Planarity : 0.004 0.058 2005 Dihedral : 5.015 24.610 1573 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.63 % Allowed : 8.62 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1501 helix: 0.25 (0.58), residues: 79 sheet: -1.47 (0.35), residues: 246 loop : -0.90 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 475 TYR 0.013 0.001 TYR C 440 PHE 0.017 0.001 PHE C 60 TRP 0.003 0.001 TRP C 491 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (11147) covalent geometry : angle 0.63412 / 0.31 (15243) SS BOND : bond 0.00275 / 0.18 ( 18) SS BOND : angle 0.89103 / 0.72 ( 36) hydrogen bonds : bond 0.03305 / 2.41 ( 128) hydrogen bonds : angle 5.75022 / 4.02 ( 279) link_BETA1-4 : bond 0.01256 / 0.65 ( 4) link_BETA1-4 : angle 4.15225 / 2.46 ( 12) link_NAG-ASN : bond 0.00432 / 0.24 ( 8) link_NAG-ASN : angle 1.58511 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.355 Fit side-chains REVERT: B 411 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8760 (t0) REVERT: B 598 MET cc_start: 0.9199 (mpp) cc_final: 0.8861 (mpp) REVERT: C 441 MET cc_start: 0.9196 (mmm) cc_final: 0.8906 (mmm) outliers start: 17 outliers final: 14 residues processed: 38 average time/residue: 0.0617 time to fit residues: 4.3525 Evaluate side-chains 39 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.043929 restraints weight = 60049.174| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.37 r_work: 0.3051 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11177 Z= 0.146 Angle : 0.574 7.679 15315 Z= 0.287 Chirality : 0.043 0.155 1887 Planarity : 0.003 0.052 2005 Dihedral : 4.674 24.216 1573 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.34 % Allowed : 9.67 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.22), residues: 1501 helix: 0.54 (0.60), residues: 79 sheet: -1.55 (0.34), residues: 252 loop : -0.80 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 475 TYR 0.007 0.001 TYR C 440 PHE 0.013 0.001 PHE C 85 TRP 0.002 0.000 TRP C 491 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11147) covalent geometry : angle 0.56048 / 0.28 (15243) SS BOND : bond 0.00223 / 0.14 ( 18) SS BOND : angle 0.76732 / 0.65 ( 36) hydrogen bonds : bond 0.02816 / 2.05 ( 128) hydrogen bonds : angle 5.36292 / 3.75 ( 279) link_BETA1-4 : bond 0.01308 / 0.67 ( 4) link_BETA1-4 : angle 4.03151 / 2.42 ( 12) link_NAG-ASN : bond 0.00244 / 0.15 ( 8) link_NAG-ASN : angle 1.25282 / 0.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.513 Fit side-chains REVERT: B 411 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8690 (t0) REVERT: B 598 MET cc_start: 0.9183 (mpp) cc_final: 0.8846 (mpp) REVERT: C 441 MET cc_start: 0.9205 (mmm) cc_final: 0.8906 (mmm) outliers start: 14 outliers final: 9 residues processed: 35 average time/residue: 0.0679 time to fit residues: 4.5586 Evaluate side-chains 34 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.060020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.043236 restraints weight = 60128.918| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.31 r_work: 0.3032 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11177 Z= 0.210 Angle : 0.615 8.004 15315 Z= 0.303 Chirality : 0.044 0.159 1887 Planarity : 0.004 0.056 2005 Dihedral : 4.794 23.750 1573 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.25 % Allowed : 10.34 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1501 helix: 0.59 (0.59), residues: 79 sheet: -1.45 (0.35), residues: 246 loop : -0.81 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 475 TYR 0.011 0.001 TYR C 440 PHE 0.022 0.001 PHE C 60 TRP 0.003 0.001 TRP C 491 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (11147) covalent geometry : angle 0.60189 / 0.30 (15243) SS BOND : bond 0.00249 / 0.16 ( 18) SS BOND : angle 0.80383 / 0.64 ( 36) hydrogen bonds : bond 0.03043 / 2.22 ( 128) hydrogen bonds : angle 5.39841 / 3.78 ( 279) link_BETA1-4 : bond 0.01258 / 0.65 ( 4) link_BETA1-4 : angle 4.04031 / 2.41 ( 12) link_NAG-ASN : bond 0.00381 / 0.21 ( 8) link_NAG-ASN : angle 1.48997 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.443 Fit side-chains REVERT: B 411 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8721 (t0) REVERT: B 598 MET cc_start: 0.9172 (mpp) cc_final: 0.8812 (mpp) REVERT: C 441 MET cc_start: 0.9192 (mmm) cc_final: 0.8885 (mmm) outliers start: 13 outliers final: 11 residues processed: 34 average time/residue: 0.0594 time to fit residues: 3.7912 Evaluate side-chains 36 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 4.9990 chunk 118 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 139 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.062158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.043757 restraints weight = 62646.428| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.58 r_work: 0.3047 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11177 Z= 0.161 Angle : 0.578 8.080 15315 Z= 0.287 Chirality : 0.043 0.153 1887 Planarity : 0.003 0.052 2005 Dihedral : 4.626 23.900 1573 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.53 % Allowed : 10.92 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1501 helix: 0.78 (0.61), residues: 79 sheet: -1.62 (0.34), residues: 252 loop : -0.73 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.008 0.001 TYR C 440 PHE 0.013 0.001 PHE C 85 TRP 0.002 0.000 TRP C 491 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11147) covalent geometry : angle 0.56457 / 0.28 (15243) SS BOND : bond 0.00238 / 0.15 ( 18) SS BOND : angle 0.81052 / 0.68 ( 36) hydrogen bonds : bond 0.02761 / 2.01 ( 128) hydrogen bonds : angle 5.23012 / 3.66 ( 279) link_BETA1-4 : bond 0.01276 / 0.66 ( 4) link_BETA1-4 : angle 3.96879 / 2.39 ( 12) link_NAG-ASN : bond 0.00258 / 0.15 ( 8) link_NAG-ASN : angle 1.27746 / 0.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.450 Fit side-chains REVERT: B 411 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8725 (t0) REVERT: B 598 MET cc_start: 0.9154 (mpp) cc_final: 0.8800 (mpp) REVERT: C 441 MET cc_start: 0.9187 (mmm) cc_final: 0.8887 (mmm) outliers start: 16 outliers final: 14 residues processed: 37 average time/residue: 0.0646 time to fit residues: 4.4786 Evaluate side-chains 39 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.062406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.044082 restraints weight = 62485.441| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.57 r_work: 0.3055 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11177 Z= 0.138 Angle : 0.556 7.640 15315 Z= 0.277 Chirality : 0.042 0.145 1887 Planarity : 0.003 0.054 2005 Dihedral : 4.459 23.152 1573 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.63 % Allowed : 10.92 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.22), residues: 1501 helix: 0.56 (0.59), residues: 85 sheet: -1.60 (0.34), residues: 252 loop : -0.70 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 475 TYR 0.007 0.001 TYR B 65 PHE 0.023 0.001 PHE C 60 TRP 0.001 0.000 TRP C 491 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11147) covalent geometry : angle 0.54352 / 0.27 (15243) SS BOND : bond 0.00211 / 0.14 ( 18) SS BOND : angle 0.70954 / 0.57 ( 36) hydrogen bonds : bond 0.02596 / 1.90 ( 128) hydrogen bonds : angle 5.01941 / 3.51 ( 279) link_BETA1-4 : bond 0.01245 / 0.64 ( 4) link_BETA1-4 : angle 3.88802 / 2.35 ( 12) link_NAG-ASN : bond 0.00223 / 0.13 ( 8) link_NAG-ASN : angle 1.14365 / 0.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.491 Fit side-chains REVERT: B 598 MET cc_start: 0.9148 (mpp) cc_final: 0.8852 (mpp) REVERT: C 441 MET cc_start: 0.9191 (mmm) cc_final: 0.8894 (mmm) outliers start: 17 outliers final: 13 residues processed: 38 average time/residue: 0.0550 time to fit residues: 3.9946 Evaluate side-chains 37 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.061395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.043096 restraints weight = 62778.597| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.52 r_work: 0.3022 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11177 Z= 0.244 Angle : 0.638 8.811 15315 Z= 0.311 Chirality : 0.044 0.159 1887 Planarity : 0.004 0.054 2005 Dihedral : 4.785 24.071 1573 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.63 % Allowed : 10.92 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.22), residues: 1501 helix: 0.30 (0.58), residues: 85 sheet: -1.61 (0.34), residues: 258 loop : -0.75 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 475 TYR 0.012 0.001 TYR C 440 PHE 0.012 0.001 PHE C 85 TRP 0.003 0.001 TRP C 491 HIS 0.003 0.001 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (11147) covalent geometry : angle 0.62608 / 0.31 (15243) SS BOND : bond 0.00293 / 0.19 ( 18) SS BOND : angle 0.83691 / 0.65 ( 36) hydrogen bonds : bond 0.03018 / 2.20 ( 128) hydrogen bonds : angle 5.33966 / 3.74 ( 279) link_BETA1-4 : bond 0.01185 / 0.61 ( 4) link_BETA1-4 : angle 3.92059 / 2.36 ( 12) link_NAG-ASN : bond 0.00438 / 0.24 ( 8) link_NAG-ASN : angle 1.50071 / 0.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.466 Fit side-chains REVERT: B 411 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8745 (t0) REVERT: B 598 MET cc_start: 0.9149 (mpp) cc_final: 0.8816 (mpp) REVERT: C 441 MET cc_start: 0.9170 (mmm) cc_final: 0.8871 (mmm) outliers start: 17 outliers final: 16 residues processed: 39 average time/residue: 0.0594 time to fit residues: 4.3920 Evaluate side-chains 41 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 140 optimal weight: 50.0000 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 50.0000 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.060716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.044068 restraints weight = 59613.124| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.40 r_work: 0.3060 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11177 Z= 0.120 Angle : 0.561 8.214 15315 Z= 0.278 Chirality : 0.043 0.155 1887 Planarity : 0.003 0.051 2005 Dihedral : 4.480 23.806 1573 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.63 % Allowed : 10.92 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1501 helix: 0.45 (0.59), residues: 85 sheet: -1.50 (0.34), residues: 263 loop : -0.67 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 480 TYR 0.008 0.001 TYR B 197 PHE 0.023 0.001 PHE C 60 TRP 0.001 0.000 TRP C 491 HIS 0.002 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11147) covalent geometry : angle 0.54895 / 0.28 (15243) SS BOND : bond 0.00210 / 0.13 ( 18) SS BOND : angle 0.71215 / 0.58 ( 36) hydrogen bonds : bond 0.02552 / 1.86 ( 128) hydrogen bonds : angle 5.03528 / 3.53 ( 279) link_BETA1-4 : bond 0.01273 / 0.65 ( 4) link_BETA1-4 : angle 3.82843 / 2.33 ( 12) link_NAG-ASN : bond 0.00220 / 0.13 ( 8) link_NAG-ASN : angle 1.11299 / 0.72 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.67 seconds wall clock time: 50 minutes 10.04 seconds (3010.04 seconds total)