Starting phenix.real_space_refine on Wed Mar 4 05:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b1d_11984/03_2026/7b1d_11984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b1d_11984/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7b1d_11984/03_2026/7b1d_11984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b1d_11984/03_2026/7b1d_11984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b1d_11984/03_2026/7b1d_11984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b1d_11984/03_2026/7b1d_11984.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.05, per 1000 atoms: 0.19 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: 0.76 Conformation dependent library (CDL) restraints added in 561.1 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: 0.39 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: 1.86 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: 6456 17.67 - 35.34: 422 35.34 - 53.01: 85 53.01 - 70.68: 18 70.68 - 88.35: 10 Dihedral angle restraints: 6991 sinusoidal: 2542 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 6988 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: 4.600 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.260 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: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 12.557 85.658 4023 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 covalent geometry : bond 0.00411 (11147) covalent geometry : angle 0.70736 (15243) SS BOND : bond 0.00418 ( 18) SS BOND : angle 0.91577 ( 36) hydrogen bonds : bond 0.24968 ( 128) hydrogen bonds : angle 8.46961 ( 279) link_BETA1-4 : bond 0.01291 ( 4) link_BETA1-4 : angle 5.30493 ( 12) link_NAG-ASN : bond 0.00147 ( 8) link_NAG-ASN : angle 1.38028 ( 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 : 0.302 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.0612 time to fit residues: 3.6703 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 : 0.388 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.062114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.045509 restraints weight = 59213.957| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.45 r_work: 0.3101 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11177 Z= 0.138 Angle : 0.594 7.734 15315 Z= 0.297 Chirality : 0.043 0.168 1887 Planarity : 0.004 0.068 2005 Dihedral : 5.835 49.947 1825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.38 % Allowed : 3.35 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.21), residues: 1501 helix: 0.21 (0.61), residues: 73 sheet: -1.20 (0.35), residues: 251 loop : -0.91 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 244 TYR 0.009 0.001 TYR C 65 PHE 0.013 0.001 PHE B 656 TRP 0.001 0.000 TRP C 491 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00313 (11147) covalent geometry : angle 0.57842 (15243) SS BOND : bond 0.00249 ( 18) SS BOND : angle 0.80843 ( 36) hydrogen bonds : bond 0.04147 ( 128) hydrogen bonds : angle 6.02403 ( 279) link_BETA1-4 : bond 0.01301 ( 4) link_BETA1-4 : angle 4.45031 ( 12) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.39597 ( 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 : 0.430 Fit side-chains REVERT: C 594 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7857 (tp) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.0642 time to fit residues: 3.5884 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 : 0.431 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 549 ASN ** B 737 ASN ** 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 = 0.3727 r_free = 0.3727 target = 0.059570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.042672 restraints weight = 61296.498| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.41 r_work: 0.2998 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.138 11177 Z= 0.425 Angle : 0.844 9.768 15315 Z= 0.401 Chirality : 0.049 0.202 1887 Planarity : 0.005 0.063 2005 Dihedral : 6.290 48.435 1825 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.96 % Allowed : 6.23 % Favored : 92.82 % 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: -1.58 (0.21), residues: 1501 helix: -0.75 (0.52), residues: 91 sheet: -1.50 (0.35), residues: 248 loop : -1.02 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 475 TYR 0.021 0.002 TYR C 440 PHE 0.020 0.002 PHE C 60 TRP 0.008 0.002 TRP C 491 HIS 0.008 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00961 (11147) covalent geometry : angle 0.82947 (15243) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.12967 ( 36) hydrogen bonds : bond 0.04419 ( 128) hydrogen bonds : angle 6.35325 ( 279) link_BETA1-4 : bond 0.01185 ( 4) link_BETA1-4 : angle 4.65836 ( 12) link_NAG-ASN : bond 0.00831 ( 8) link_NAG-ASN : angle 2.17597 ( 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 34 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.327 Fit side-chains REVERT: B 598 MET cc_start: 0.9225 (mpp) cc_final: 0.8913 (mpp) REVERT: B 624 MET cc_start: 0.8160 (pmm) cc_final: 0.7950 (pmm) REVERT: C 441 MET cc_start: 0.9210 (mmm) cc_final: 0.8926 (mmm) REVERT: C 594 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (tp) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0674 time to fit residues: 4.0823 Evaluate side-chains 33 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 148 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 140 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.061067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.044404 restraints weight = 59977.261| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.39 r_work: 0.3062 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11177 Z= 0.130 Angle : 0.581 7.736 15315 Z= 0.290 Chirality : 0.043 0.165 1887 Planarity : 0.004 0.056 2005 Dihedral : 5.652 47.592 1825 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.05 % Allowed : 7.66 % Favored : 91.28 % 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: -1.35 (0.22), residues: 1501 helix: 0.04 (0.58), residues: 85 sheet: -1.50 (0.34), residues: 254 loop : -0.86 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 137 TYR 0.008 0.001 TYR C 226 PHE 0.014 0.001 PHE B 656 TRP 0.003 0.000 TRP C 491 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00289 (11147) covalent geometry : angle 0.56514 (15243) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.79056 ( 36) hydrogen bonds : bond 0.03050 ( 128) hydrogen bonds : angle 5.58321 ( 279) link_BETA1-4 : bond 0.01291 ( 4) link_BETA1-4 : angle 4.42994 ( 12) link_NAG-ASN : bond 0.00273 ( 8) link_NAG-ASN : angle 1.27314 ( 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 35 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.490 Fit side-chains REVERT: B 598 MET cc_start: 0.9198 (mpp) cc_final: 0.8904 (mpp) REVERT: B 624 MET cc_start: 0.8119 (pmm) cc_final: 0.7879 (pmm) REVERT: C 441 MET cc_start: 0.9215 (mmm) cc_final: 0.8924 (mmm) REVERT: C 594 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7941 (tp) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.0676 time to fit residues: 4.3425 Evaluate side-chains 32 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 594 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: 6.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN B 288 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 554 HIS ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.059171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.042300 restraints weight = 60554.391| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.43 r_work: 0.2989 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 11177 Z= 0.367 Angle : 0.772 9.405 15315 Z= 0.371 Chirality : 0.047 0.184 1887 Planarity : 0.004 0.060 2005 Dihedral : 6.099 48.433 1825 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 1.63 % Allowed : 8.91 % Favored : 89.46 % 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: -1.53 (0.22), residues: 1501 helix: -0.35 (0.54), residues: 85 sheet: -1.58 (0.35), residues: 243 loop : -0.99 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 475 TYR 0.019 0.002 TYR C 440 PHE 0.020 0.002 PHE C 60 TRP 0.006 0.001 TRP C 491 HIS 0.006 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00831 (11147) covalent geometry : angle 0.75636 (15243) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.04178 ( 36) hydrogen bonds : bond 0.03824 ( 128) hydrogen bonds : angle 6.05867 ( 279) link_BETA1-4 : bond 0.01259 ( 4) link_BETA1-4 : angle 4.70500 ( 12) link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 2.00804 ( 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 : 0.365 Fit side-chains REVERT: B 411 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8834 (t0) REVERT: B 598 MET cc_start: 0.9200 (mpp) cc_final: 0.8854 (mpp) REVERT: B 624 MET cc_start: 0.8126 (pmm) cc_final: 0.7870 (pmm) REVERT: C 441 MET cc_start: 0.9216 (mmm) cc_final: 0.8911 (mmm) outliers start: 17 outliers final: 12 residues processed: 38 average time/residue: 0.0668 time to fit residues: 4.6846 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 : 0.425 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 0.0020 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.061235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.044624 restraints weight = 59885.344| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.47 r_work: 0.3078 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11177 Z= 0.097 Angle : 0.562 7.781 15315 Z= 0.282 Chirality : 0.042 0.153 1887 Planarity : 0.003 0.050 2005 Dihedral : 5.435 47.860 1825 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.05 % Allowed : 9.29 % Favored : 89.66 % 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: 0.34 (0.59), residues: 85 sheet: -1.56 (0.34), residues: 252 loop : -0.77 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 475 TYR 0.008 0.001 TYR B 65 PHE 0.013 0.001 PHE C 277 TRP 0.002 0.000 TRP B 491 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00217 (11147) covalent geometry : angle 0.54674 (15243) SS BOND : bond 0.00218 ( 18) SS BOND : angle 0.71516 ( 36) hydrogen bonds : bond 0.02645 ( 128) hydrogen bonds : angle 5.28007 ( 279) link_BETA1-4 : bond 0.01308 ( 4) link_BETA1-4 : angle 4.41361 ( 12) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 1.06046 ( 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 35 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.364 Fit side-chains REVERT: B 598 MET cc_start: 0.9142 (mpp) cc_final: 0.8832 (mpp) REVERT: B 624 MET cc_start: 0.8172 (pmm) cc_final: 0.7904 (pmm) REVERT: C 441 MET cc_start: 0.9259 (mmm) cc_final: 0.8951 (mmm) outliers start: 11 outliers final: 9 residues processed: 32 average time/residue: 0.0665 time to fit residues: 4.0222 Evaluate side-chains 33 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL 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 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: 4.9990 chunk 43 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3748 r_free = 0.3748 target = 0.060151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.043247 restraints weight = 60073.156| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.48 r_work: 0.3034 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11177 Z= 0.212 Angle : 0.609 8.434 15315 Z= 0.300 Chirality : 0.044 0.159 1887 Planarity : 0.004 0.058 2005 Dihedral : 5.537 48.672 1825 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.25 % Allowed : 9.87 % Favored : 88.89 % 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: -1.24 (0.22), residues: 1501 helix: 0.33 (0.58), residues: 85 sheet: -1.44 (0.35), residues: 246 loop : -0.80 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 475 TYR 0.012 0.001 TYR C 440 PHE 0.020 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 covalent geometry : bond 0.00481 (11147) covalent geometry : angle 0.59309 (15243) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.78777 ( 36) hydrogen bonds : bond 0.02961 ( 128) hydrogen bonds : angle 5.40512 ( 279) link_BETA1-4 : bond 0.01298 ( 4) link_BETA1-4 : angle 4.50206 ( 12) link_NAG-ASN : bond 0.00350 ( 8) link_NAG-ASN : angle 1.44556 ( 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 : 0.505 Fit side-chains REVERT: B 411 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8735 (t0) REVERT: B 598 MET cc_start: 0.9192 (mpp) cc_final: 0.8853 (mpp) REVERT: B 624 MET cc_start: 0.8164 (pmm) cc_final: 0.7885 (pmm) REVERT: C 441 MET cc_start: 0.9239 (mmm) cc_final: 0.8902 (mmm) outliers start: 13 outliers final: 11 residues processed: 34 average time/residue: 0.0694 time to fit residues: 4.4745 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 : 0.468 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 118 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 139 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3766 r_free = 0.3766 target = 0.060919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.044331 restraints weight = 59568.718| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.43 r_work: 0.3069 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11177 Z= 0.123 Angle : 0.549 7.837 15315 Z= 0.274 Chirality : 0.042 0.149 1887 Planarity : 0.003 0.050 2005 Dihedral : 5.321 48.422 1825 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.34 % Allowed : 10.25 % 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: -1.16 (0.22), residues: 1501 helix: 0.56 (0.60), residues: 85 sheet: -1.52 (0.34), residues: 257 loop : -0.71 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 480 TYR 0.007 0.001 TYR B 65 PHE 0.012 0.001 PHE C 85 TRP 0.001 0.000 TRP B 491 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00283 (11147) covalent geometry : angle 0.53346 (15243) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.68329 ( 36) hydrogen bonds : bond 0.02568 ( 128) hydrogen bonds : angle 5.10028 ( 279) link_BETA1-4 : bond 0.01291 ( 4) link_BETA1-4 : angle 4.37458 ( 12) link_NAG-ASN : bond 0.00204 ( 8) link_NAG-ASN : angle 1.12516 ( 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 38 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.423 Fit side-chains REVERT: B 598 MET cc_start: 0.9163 (mpp) cc_final: 0.8831 (mpp) REVERT: B 624 MET cc_start: 0.8161 (pmm) cc_final: 0.7888 (pmm) REVERT: C 146 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8746 (mtm) REVERT: C 441 MET cc_start: 0.9236 (mmm) cc_final: 0.8917 (mmm) outliers start: 14 outliers final: 12 residues processed: 35 average time/residue: 0.0639 time to fit residues: 4.2705 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 : 0.350 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 103 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN B 478 HIS ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.061850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.045434 restraints weight = 59286.275| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.37 r_work: 0.3110 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11177 Z= 0.083 Angle : 0.524 7.565 15315 Z= 0.262 Chirality : 0.042 0.147 1887 Planarity : 0.003 0.053 2005 Dihedral : 4.993 50.272 1825 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.77 % Allowed : 10.92 % Favored : 88.31 % 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: -1.09 (0.22), residues: 1501 helix: 0.76 (0.61), residues: 86 sheet: -1.35 (0.35), residues: 254 loop : -0.71 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 110 TYR 0.008 0.001 TYR B 197 PHE 0.023 0.001 PHE C 60 TRP 0.002 0.000 TRP B 491 HIS 0.002 0.000 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00186 (11147) covalent geometry : angle 0.50889 (15243) SS BOND : bond 0.00159 ( 18) SS BOND : angle 0.60420 ( 36) hydrogen bonds : bond 0.02260 ( 128) hydrogen bonds : angle 4.65994 ( 279) link_BETA1-4 : bond 0.01340 ( 4) link_BETA1-4 : angle 4.26887 ( 12) link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 0.96846 ( 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 31 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.281 Fit side-chains REVERT: B 598 MET cc_start: 0.9180 (mpp) cc_final: 0.8844 (mpp) REVERT: B 624 MET cc_start: 0.8076 (pmm) cc_final: 0.7812 (pmm) REVERT: C 441 MET cc_start: 0.9250 (mmm) cc_final: 0.8935 (mmm) outliers start: 8 outliers final: 7 residues processed: 29 average time/residue: 0.0651 time to fit residues: 3.7130 Evaluate side-chains 30 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 548 ILE 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 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: 8.9990 chunk 112 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.060207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.042012 restraints weight = 63312.414| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.38 r_work: 0.2977 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.141 11177 Z= 0.449 Angle : 0.853 9.503 15315 Z= 0.407 Chirality : 0.049 0.183 1887 Planarity : 0.004 0.058 2005 Dihedral : 6.063 48.279 1825 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.96 % Allowed : 10.82 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1501 helix: -0.46 (0.53), residues: 91 sheet: -1.47 (0.34), residues: 260 loop : -0.94 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 475 TYR 0.023 0.002 TYR C 440 PHE 0.016 0.002 PHE B 55 TRP 0.007 0.002 TRP C 491 HIS 0.006 0.002 HIS B 662 Details of bonding type rmsd covalent geometry : bond 0.01005 (11147) covalent geometry : angle 0.83963 (15243) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.06721 ( 36) hydrogen bonds : bond 0.03828 ( 128) hydrogen bonds : angle 5.84654 ( 279) link_BETA1-4 : bond 0.01217 ( 4) link_BETA1-4 : angle 4.60797 ( 12) link_NAG-ASN : bond 0.00863 ( 8) link_NAG-ASN : angle 2.16572 ( 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 33 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.268 Fit side-chains REVERT: B 624 MET cc_start: 0.8100 (pmm) cc_final: 0.7808 (pmm) outliers start: 10 outliers final: 10 residues processed: 31 average time/residue: 0.0564 time to fit residues: 3.2923 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 : 0.437 ------------------------------------------------------------------------------- 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 548 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 140 optimal weight: 50.0000 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 50.0000 chunk 107 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.060835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.044218 restraints weight = 59420.524| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.39 r_work: 0.3065 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11177 Z= 0.107 Angle : 0.560 7.743 15315 Z= 0.281 Chirality : 0.043 0.154 1887 Planarity : 0.003 0.050 2005 Dihedral : 5.430 46.808 1825 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.05 % Allowed : 10.82 % Favored : 88.12 % 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: -1.18 (0.23), residues: 1501 helix: 0.19 (0.58), residues: 91 sheet: -1.55 (0.35), residues: 247 loop : -0.70 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 480 TYR 0.010 0.001 TYR B 197 PHE 0.021 0.001 PHE C 60 TRP 0.001 0.000 TRP C 491 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00243 (11147) covalent geometry : angle 0.54550 (15243) SS BOND : bond 0.00189 ( 18) SS BOND : angle 0.67884 ( 36) hydrogen bonds : bond 0.02577 ( 128) hydrogen bonds : angle 5.14521 ( 279) link_BETA1-4 : bond 0.01269 ( 4) link_BETA1-4 : angle 4.28096 ( 12) link_NAG-ASN : bond 0.00230 ( 8) link_NAG-ASN : angle 1.03517 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.31 seconds wall clock time: 54 minutes 57.80 seconds (3297.80 seconds total)