Starting phenix.real_space_refine on Tue Jul 29 07:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_11984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_11984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_11984.map" model { file = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_11984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b1d_11984/07_2025/7b1d_11984.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 13, 'ASP:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} 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: {'GLN:plan1': 22, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 1, 'HIS:plan': 10, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 13} 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: 7.68, per 1000 atoms: 0.70 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: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.28 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: 3.52 Time building geometry restraints manager: 3.07 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 784 or resid 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 784 or resid 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: 4.050 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.090 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (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 TRP 0.002 0.001 TRP B 491 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE C 85 TYR 0.014 0.001 TYR B 138 ARG 0.002 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 8) link_NAG-ASN : angle 1.38028 ( 24) link_BETA1-4 : bond 0.01291 ( 4) link_BETA1-4 : angle 5.30493 ( 12) hydrogen bonds : bond 0.24968 ( 128) hydrogen bonds : angle 8.46961 ( 279) SS BOND : bond 0.00418 ( 18) SS BOND : angle 0.91577 ( 36) covalent geometry : bond 0.00411 (11147) covalent geometry : angle 0.70736 (15243) *********************** 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 : 1.198 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.2057 time to fit residues: 13.4477 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 : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.0470 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3760 r_free = 0.3760 target = 0.060743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.043945 restraints weight = 60048.967| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.39 r_work: 0.3050 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 11177 Z= 0.276 Angle : 0.708 8.398 15315 Z= 0.345 Chirality : 0.046 0.190 1887 Planarity : 0.004 0.067 2005 Dihedral : 6.072 48.389 1825 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.38 % Allowed : 4.31 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1501 helix: -0.29 (0.57), residues: 79 sheet: -1.51 (0.34), residues: 247 loop : -0.93 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 491 HIS 0.005 0.001 HIS B 54 PHE 0.016 0.002 PHE B 656 TYR 0.016 0.002 TYR C 440 ARG 0.007 0.001 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 8) link_NAG-ASN : angle 1.86652 ( 24) link_BETA1-4 : bond 0.01178 ( 4) link_BETA1-4 : angle 4.59218 ( 12) hydrogen bonds : bond 0.04103 ( 128) hydrogen bonds : angle 6.15431 ( 279) SS BOND : bond 0.00306 ( 18) SS BOND : angle 0.94554 ( 36) covalent geometry : bond 0.00627 (11147) covalent geometry : angle 0.69247 (15243) *********************** 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 : 1.264 Fit side-chains REVERT: C 594 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7937 (tp) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.1563 time to fit residues: 8.9392 Evaluate side-chains 28 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.061096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.044461 restraints weight = 60020.439| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.44 r_work: 0.3067 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11177 Z= 0.173 Angle : 0.596 8.979 15315 Z= 0.296 Chirality : 0.043 0.167 1887 Planarity : 0.004 0.056 2005 Dihedral : 5.648 48.708 1825 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.05 % Allowed : 6.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1501 helix: 0.06 (0.59), residues: 79 sheet: -1.43 (0.36), residues: 237 loop : -0.88 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 491 HIS 0.003 0.001 HIS B 54 PHE 0.017 0.001 PHE C 60 TYR 0.009 0.001 TYR C 440 ARG 0.001 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 8) link_NAG-ASN : angle 1.35613 ( 24) link_BETA1-4 : bond 0.01268 ( 4) link_BETA1-4 : angle 4.45849 ( 12) hydrogen bonds : bond 0.03491 ( 128) hydrogen bonds : angle 5.62730 ( 279) SS BOND : bond 0.00251 ( 18) SS BOND : angle 0.79419 ( 36) covalent geometry : bond 0.00394 (11147) covalent geometry : angle 0.58036 (15243) *********************** 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 36 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 1.492 Fit side-chains REVERT: B 669 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7710 (m) REVERT: C 441 MET cc_start: 0.9200 (mmm) cc_final: 0.8941 (mmm) REVERT: C 594 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7946 (tp) outliers start: 11 outliers final: 5 residues processed: 33 average time/residue: 0.1997 time to fit residues: 13.2620 Evaluate side-chains 31 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 702 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 99 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 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 = 0.3767 r_free = 0.3767 target = 0.060833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.044271 restraints weight = 59296.282| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.32 r_work: 0.3065 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1324 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= 0.170 Angle : 0.586 8.008 15315 Z= 0.290 Chirality : 0.043 0.158 1887 Planarity : 0.004 0.057 2005 Dihedral : 5.434 48.965 1825 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.44 % Allowed : 7.18 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1501 helix: 0.22 (0.58), residues: 85 sheet: -1.32 (0.35), residues: 249 loop : -0.85 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 491 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE C 85 TYR 0.009 0.001 TYR C 440 ARG 0.002 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 1.34861 ( 24) link_BETA1-4 : bond 0.01286 ( 4) link_BETA1-4 : angle 4.45150 ( 12) hydrogen bonds : bond 0.03021 ( 128) hydrogen bonds : angle 5.34106 ( 279) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.72447 ( 36) covalent geometry : bond 0.00390 (11147) covalent geometry : angle 0.57058 (15243) *********************** 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 39 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 1.406 Fit side-chains REVERT: B 598 MET cc_start: 0.9170 (mpp) cc_final: 0.8915 (mpp) REVERT: B 669 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7719 (t) REVERT: C 441 MET cc_start: 0.9216 (mmm) cc_final: 0.8925 (mmm) outliers start: 15 outliers final: 10 residues processed: 36 average time/residue: 0.1825 time to fit residues: 12.5496 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 : 1.461 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 688 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 319 VAL Chi-restraints excluded: chain C residue 366 VAL 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 78 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 136 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.3380 ------------------------------------------------------------------------------- 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 688 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 = 0.3780 r_free = 0.3780 target = 0.061450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.044925 restraints weight = 59286.452| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.38 r_work: 0.3084 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1404 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 : 0.551 7.744 15315 Z= 0.274 Chirality : 0.042 0.149 1887 Planarity : 0.003 0.052 2005 Dihedral : 5.224 49.293 1825 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.25 % Allowed : 8.62 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1501 helix: 0.41 (0.60), residues: 85 sheet: -1.19 (0.35), residues: 249 loop : -0.79 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 491 HIS 0.002 0.001 HIS B 54 PHE 0.019 0.001 PHE C 60 TYR 0.008 0.001 TYR B 65 ARG 0.001 0.000 ARG C 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.13472 ( 24) link_BETA1-4 : bond 0.01314 ( 4) link_BETA1-4 : angle 4.39969 ( 12) hydrogen bonds : bond 0.02709 ( 128) hydrogen bonds : angle 5.08170 ( 279) SS BOND : bond 0.00213 ( 18) SS BOND : angle 0.70675 ( 36) covalent geometry : bond 0.00275 (11147) covalent geometry : angle 0.53520 (15243) *********************** 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 37 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 1.184 Fit side-chains REVERT: B 598 MET cc_start: 0.9192 (mpp) cc_final: 0.8906 (mpp) REVERT: B 669 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7486 (m) REVERT: C 441 MET cc_start: 0.9209 (mmm) cc_final: 0.8916 (mmm) outliers start: 13 outliers final: 10 residues processed: 34 average time/residue: 0.1472 time to fit residues: 9.7746 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 : 1.153 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 688 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 319 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 83 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.060510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043559 restraints weight = 59938.668| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.50 r_work: 0.3035 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11177 Z= 0.225 Angle : 0.619 8.354 15315 Z= 0.303 Chirality : 0.044 0.159 1887 Planarity : 0.004 0.057 2005 Dihedral : 5.463 48.706 1825 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.44 % Allowed : 9.39 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1501 helix: 0.33 (0.58), residues: 85 sheet: -1.25 (0.35), residues: 249 loop : -0.79 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 491 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE B 656 TYR 0.012 0.001 TYR C 440 ARG 0.003 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 8) link_NAG-ASN : angle 1.46054 ( 24) link_BETA1-4 : bond 0.01278 ( 4) link_BETA1-4 : angle 4.45869 ( 12) hydrogen bonds : bond 0.03020 ( 128) hydrogen bonds : angle 5.33856 ( 279) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.81864 ( 36) covalent geometry : bond 0.00513 (11147) covalent geometry : angle 0.60365 (15243) *********************** 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 39 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 1.311 Fit side-chains REVERT: B 411 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8781 (t0) REVERT: B 598 MET cc_start: 0.9231 (mpp) cc_final: 0.8877 (mpp) REVERT: B 669 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7767 (t) REVERT: C 441 MET cc_start: 0.9246 (mmm) cc_final: 0.8942 (mmm) outliers start: 15 outliers final: 10 residues processed: 36 average time/residue: 0.1510 time to fit residues: 10.5723 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 : 1.237 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 2.9990 chunk 133 optimal weight: 50.0000 chunk 64 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 0.1980 chunk 145 optimal weight: 40.0000 chunk 122 optimal weight: 8.9990 chunk 73 optimal weight: 0.0010 chunk 48 optimal weight: 0.7980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 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 = 0.3784 r_free = 0.3784 target = 0.061573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045066 restraints weight = 60372.078| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.42 r_work: 0.3087 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1642 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= 0.097 Angle : 0.537 7.522 15315 Z= 0.268 Chirality : 0.042 0.151 1887 Planarity : 0.003 0.049 2005 Dihedral : 5.145 48.712 1825 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.15 % Allowed : 9.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1501 helix: 0.69 (0.61), residues: 85 sheet: -1.32 (0.35), residues: 254 loop : -0.72 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 491 HIS 0.002 0.000 HIS B 395 PHE 0.020 0.001 PHE C 60 TYR 0.008 0.001 TYR B 65 ARG 0.001 0.000 ARG B 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 0.99857 ( 24) link_BETA1-4 : bond 0.01319 ( 4) link_BETA1-4 : angle 4.30941 ( 12) hydrogen bonds : bond 0.02453 ( 128) hydrogen bonds : angle 4.87788 ( 279) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.65678 ( 36) covalent geometry : bond 0.00221 (11147) covalent geometry : angle 0.52227 (15243) *********************** 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 36 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 1.190 Fit side-chains REVERT: B 669 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7629 (t) REVERT: C 441 MET cc_start: 0.9243 (mmm) cc_final: 0.8944 (mmm) outliers start: 12 outliers final: 10 residues processed: 33 average time/residue: 0.1493 time to fit residues: 9.6610 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 : 1.181 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 688 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 319 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 120 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 135 optimal weight: 40.0000 chunk 91 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 147 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.061306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.044810 restraints weight = 58880.211| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.34 r_work: 0.3083 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11177 Z= 0.120 Angle : 0.540 8.431 15315 Z= 0.268 Chirality : 0.042 0.143 1887 Planarity : 0.003 0.054 2005 Dihedral : 5.087 49.398 1825 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.15 % Allowed : 10.06 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1501 helix: 0.66 (0.61), residues: 85 sheet: -1.29 (0.35), residues: 254 loop : -0.71 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 491 HIS 0.002 0.000 HIS B 54 PHE 0.012 0.001 PHE C 85 TYR 0.008 0.001 TYR B 65 ARG 0.002 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 1.12293 ( 24) link_BETA1-4 : bond 0.01295 ( 4) link_BETA1-4 : angle 4.30883 ( 12) hydrogen bonds : bond 0.02467 ( 128) hydrogen bonds : angle 4.81473 ( 279) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.66490 ( 36) covalent geometry : bond 0.00277 (11147) covalent geometry : angle 0.52449 (15243) *********************** 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 36 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 1.213 Fit side-chains REVERT: B 669 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7576 (t) REVERT: C 441 MET cc_start: 0.9236 (mmm) cc_final: 0.8927 (mmm) outliers start: 12 outliers final: 11 residues processed: 33 average time/residue: 0.1531 time to fit residues: 9.8578 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 : 1.178 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 688 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 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 53 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.061949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.043645 restraints weight = 62992.381| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.55 r_work: 0.3041 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 11177 Z= 0.228 Angle : 0.620 9.001 15315 Z= 0.302 Chirality : 0.043 0.153 1887 Planarity : 0.004 0.053 2005 Dihedral : 5.396 48.275 1825 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.34 % Allowed : 9.96 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1501 helix: 0.47 (0.59), residues: 85 sheet: -1.45 (0.34), residues: 255 loop : -0.71 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 491 HIS 0.003 0.001 HIS B 54 PHE 0.021 0.001 PHE C 60 TYR 0.012 0.001 TYR C 440 ARG 0.004 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 8) link_NAG-ASN : angle 1.41451 ( 24) link_BETA1-4 : bond 0.01151 ( 4) link_BETA1-4 : angle 4.34023 ( 12) hydrogen bonds : bond 0.02905 ( 128) hydrogen bonds : angle 5.16718 ( 279) SS BOND : bond 0.00269 ( 18) SS BOND : angle 0.80692 ( 36) covalent geometry : bond 0.00515 (11147) covalent geometry : angle 0.60505 (15243) *********************** 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 37 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 1.401 Fit side-chains REVERT: B 411 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8764 (t0) REVERT: B 669 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7709 (t) REVERT: C 441 MET cc_start: 0.9237 (mmm) cc_final: 0.8945 (mmm) outliers start: 14 outliers final: 10 residues processed: 34 average time/residue: 0.1617 time to fit residues: 10.7217 Evaluate side-chains 35 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR 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 14 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 5 optimal weight: 0.0470 chunk 57 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.0050 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.061528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.045032 restraints weight = 59607.254| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.43 r_work: 0.3095 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1844 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= 0.087 Angle : 0.538 8.906 15315 Z= 0.267 Chirality : 0.042 0.145 1887 Planarity : 0.003 0.050 2005 Dihedral : 5.094 48.625 1825 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.15 % Allowed : 10.15 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1501 helix: 0.72 (0.61), residues: 85 sheet: -1.32 (0.34), residues: 259 loop : -0.66 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 491 HIS 0.002 0.001 HIS B 395 PHE 0.012 0.001 PHE C 85 TYR 0.008 0.001 TYR B 65 ARG 0.001 0.000 ARG B 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 0.99810 ( 24) link_BETA1-4 : bond 0.01288 ( 4) link_BETA1-4 : angle 4.22979 ( 12) hydrogen bonds : bond 0.02364 ( 128) hydrogen bonds : angle 4.75684 ( 279) SS BOND : bond 0.00191 ( 18) SS BOND : angle 0.64150 ( 36) covalent geometry : bond 0.00194 (11147) covalent geometry : angle 0.52329 (15243) ********************** 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 36 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 1.397 Fit side-chains REVERT: B 411 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 669 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7621 (t) REVERT: C 146 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8739 (mtm) REVERT: C 441 MET cc_start: 0.9247 (mmm) cc_final: 0.8950 (mmm) outliers start: 12 outliers final: 9 residues processed: 33 average time/residue: 0.2251 time to fit residues: 13.6781 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 : 1.256 ------------------------------------------------------------------------------- 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 646 LEU Chi-restraints excluded: chain B residue 669 THR 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 97 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 137 optimal weight: 50.0000 chunk 139 optimal weight: 0.9980 chunk 138 optimal weight: 50.0000 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 145 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 130 optimal weight: 0.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.060900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044141 restraints weight = 59350.432| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.41 r_work: 0.3063 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11177 Z= 0.157 Angle : 0.561 8.579 15315 Z= 0.276 Chirality : 0.042 0.144 1887 Planarity : 0.003 0.053 2005 Dihedral : 5.161 48.760 1825 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1501 helix: 0.67 (0.60), residues: 85 sheet: -1.37 (0.34), residues: 260 loop : -0.65 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 491 HIS 0.002 0.001 HIS B 416 PHE 0.022 0.001 PHE C 60 TYR 0.008 0.001 TYR C 440 ARG 0.002 0.000 ARG C 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 1.20334 ( 24) link_BETA1-4 : bond 0.01293 ( 4) link_BETA1-4 : angle 4.27297 ( 12) hydrogen bonds : bond 0.02563 ( 128) hydrogen bonds : angle 4.85904 ( 279) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.68888 ( 36) covalent geometry : bond 0.00360 (11147) covalent geometry : angle 0.54615 (15243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7869.51 seconds wall clock time: 141 minutes 56.24 seconds (8516.24 seconds total)