Starting phenix.real_space_refine on Fri Jun 6 09:40:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3x_32295/06_2025/7w3x_32295.cif" } resolution = 3.21 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= 0.002 sd= 0.033 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 32 5.16 5 C 4709 2.51 5 N 1199 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7429 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 7025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7025 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 855} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.89, per 1000 atoms: 0.66 Number of scatterers: 7429 At special positions: 0 Unit cell: (100.885, 93.0579, 130.455, 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 32 16.00 O 1489 8.00 N 1199 7.00 C 4709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 764 " 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 ALPHA1-2 " MAN A 5 " - " MAN A 6 " ALPHA1-3 " BMA A 3 " - " MAN A 8 " " MAN A 4 " - " MAN A 7 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA A 3 " - " MAN A 4 " " MAN A 4 " - " MAN A 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 1 " - " ASN C 143 " " NAG B 1 " - " ASN C 311 " " NAG C1001 " - " ASN C 73 " " NAG C1002 " - " ASN C 159 " " NAG C1003 " - " ASN C 234 " " NAG C1004 " - " ASN C 261 " " NAG C1005 " - " ASN C 481 " " NAG C1006 " - " ASN C 532 " " NAG C1007 " - " ASN C 542 " " NAG C1008 " - " ASN C 591 " " NAG C1009 " - " ASN C 767 " " NAG C1010 " - " ASN C 888 " " NAG C1011 " - " ASN C 855 " " NAG D 1 " - " ASN C 562 " " NAG E 1 " - " ASN C 647 " " NAG F 1 " - " ASN C 848 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 873.1 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 20.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.659A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.850A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.703A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.734A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.502A pdb=" N SER C 182 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 removed outlier: 3.567A pdb=" N GLU C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.607A pdb=" N GLY C 310 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 311 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 312 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.778A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.726A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.878A pdb=" N SER C 480 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.717A pdb=" N LEU C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN C 528 " --> pdb=" O LYS C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 666 through 672 removed outlier: 3.848A pdb=" N GLY C 670 " --> pdb=" O GLN C 667 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.718A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.802A pdb=" N LEU C 744 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 745 " --> pdb=" O CYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 768 Processing helix chain 'C' and resid 802 through 811 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 883 through 889 Processing helix chain 'C' and resid 917 through 921 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.164A pdb=" N THR C 101 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.485A pdb=" N GLU C 71 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 80 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP C 118 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 243 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 269 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 293 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 561 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 606 " --> pdb=" O ASP C 631 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 726 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 750 " --> pdb=" O ASP C 824 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 823 " --> pdb=" O ASN C 848 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 151 removed outlier: 4.158A pdb=" N GLY C 151 " --> pdb=" O ASN C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 328 removed outlier: 5.969A pdb=" N GLN C 327 " --> pdb=" O PHE C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.544A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 377 through 378 removed outlier: 7.293A pdb=" N GLN C 399 " --> pdb=" O GLY C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 569 through 570 removed outlier: 3.928A pdb=" N GLY C 570 " --> pdb=" O ASN C 591 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 614 through 616 removed outlier: 5.537A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 687 through 688 removed outlier: 5.958A pdb=" N GLY C 687 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ARG C 711 " --> pdb=" O GLY C 687 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU C 708 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C 734 " --> pdb=" O LEU C 708 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 710 " --> pdb=" O TYR C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 758 through 759 removed outlier: 3.707A pdb=" N GLY C 759 " --> pdb=" O LYS C 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 782 through 788 Processing sheet with id=AB3, first strand: chain 'C' and resid 855 through 856 removed outlier: 4.920A pdb=" N GLY C 856 " --> pdb=" O SER C 879 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU C 878 " --> pdb=" O HIS C 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 870 through 872 removed outlier: 6.953A pdb=" N LEU C 871 " --> pdb=" O ASP C 896 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 104 hydrogen bonds defined for protein. 180 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: 2.72 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2327 1.34 - 1.46: 1499 1.46 - 1.58: 3698 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7572 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" C1 NAG C1008 " pdb=" O5 NAG C1008 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" CA THR C 101 " pdb=" CB THR C 101 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.72e+00 bond pdb=" C1 NAG C1004 " pdb=" O5 NAG C1004 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C1 NAG C1005 " pdb=" O5 NAG C1005 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9802 1.62 - 3.25: 353 3.25 - 4.87: 74 4.87 - 6.50: 21 6.50 - 8.12: 5 Bond angle restraints: 10255 Sorted by residual: angle pdb=" N VAL C 486 " pdb=" CA VAL C 486 " pdb=" C VAL C 486 " ideal model delta sigma weight residual 113.20 109.87 3.33 9.60e-01 1.09e+00 1.20e+01 angle pdb=" N ILE C 538 " pdb=" CA ILE C 538 " pdb=" C ILE C 538 " ideal model delta sigma weight residual 111.77 108.26 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA GLU C 123 " pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" C3 MAN A 5 " pdb=" C2 MAN A 5 " pdb=" O2 MAN A 5 " ideal model delta sigma weight residual 111.77 103.65 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" C TRP C 67 " pdb=" CA TRP C 67 " pdb=" CB TRP C 67 " ideal model delta sigma weight residual 109.80 112.86 -3.06 1.23e+00 6.61e-01 6.19e+00 ... (remaining 10250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 4567 23.08 - 46.17: 294 46.17 - 69.25: 34 69.25 - 92.33: 30 92.33 - 115.41: 33 Dihedral angle restraints: 4958 sinusoidal: 2379 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS C 90 " pdb=" SG CYS C 90 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual -86.00 -162.81 76.81 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS C 621 " pdb=" SG CYS C 621 " pdb=" SG CYS C 644 " pdb=" CB CYS C 644 " ideal model delta sinusoidal sigma weight residual 93.00 17.31 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA ASN C 261 " pdb=" C ASN C 261 " pdb=" N PHE C 262 " pdb=" CA PHE C 262 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 4955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 969 0.055 - 0.110: 230 0.110 - 0.165: 45 0.165 - 0.220: 5 0.220 - 0.274: 4 Chirality restraints: 1253 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1250 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 67 " -0.042 2.00e-02 2.50e+03 3.93e-02 3.87e+01 pdb=" CG TRP C 67 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP C 67 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP C 67 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 67 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 67 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP C 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 767 " 0.005 2.00e-02 2.50e+03 2.38e-02 7.06e+00 pdb=" CG ASN C 767 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 767 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 767 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C1009 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " -0.002 2.00e-02 2.50e+03 1.62e-02 3.30e+00 pdb=" CG ASN C 261 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C1004 " -0.016 2.00e-02 2.50e+03 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 472 2.73 - 3.27: 7470 3.27 - 3.82: 11515 3.82 - 4.36: 14467 4.36 - 4.90: 24164 Nonbonded interactions: 58088 Sorted by model distance: nonbonded pdb=" O PHE C 260 " pdb=" OG SER C 263 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASP C 394 " pdb=" OG SER C 396 " model vdw 2.254 3.040 nonbonded pdb=" OE1 GLU C 461 " pdb=" OH TYR C 792 " model vdw 2.255 3.040 nonbonded pdb=" OG SER C 46 " pdb=" O THR C 101 " model vdw 2.264 3.040 nonbonded pdb=" O4 NAG C1011 " pdb=" O7 NAG C1011 " model vdw 2.285 3.040 ... (remaining 58083 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 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 0.056 7607 Z= 0.218 Angle : 0.819 16.710 10356 Z= 0.379 Chirality : 0.051 0.274 1253 Planarity : 0.004 0.044 1270 Dihedral : 18.428 115.413 3282 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.28), residues: 889 helix: -2.51 (0.40), residues: 145 sheet: -2.57 (0.39), residues: 169 loop : -1.63 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.003 TRP C 67 HIS 0.004 0.001 HIS C 609 PHE 0.019 0.002 PHE C 262 TYR 0.016 0.002 TYR C 813 ARG 0.003 0.000 ARG C 794 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 16) link_NAG-ASN : angle 4.02170 ( 48) link_ALPHA1-6 : bond 0.00333 ( 3) link_ALPHA1-6 : angle 1.75483 ( 9) link_BETA1-4 : bond 0.00631 ( 8) link_BETA1-4 : angle 1.88281 ( 24) link_ALPHA1-2 : bond 0.00046 ( 1) link_ALPHA1-2 : angle 2.56514 ( 3) link_ALPHA1-3 : bond 0.00347 ( 3) link_ALPHA1-3 : angle 1.62964 ( 9) hydrogen bonds : bond 0.25490 ( 104) hydrogen bonds : angle 7.43720 ( 180) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.44471 ( 8) covalent geometry : bond 0.00450 ( 7572) covalent geometry : angle 0.76489 (10255) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.7323 (tp30) cc_final: 0.7053 (tp30) REVERT: C 131 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7869 (mtp85) REVERT: C 218 SER cc_start: 0.8101 (t) cc_final: 0.7313 (m) REVERT: C 272 SER cc_start: 0.8059 (p) cc_final: 0.7830 (p) REVERT: C 668 SER cc_start: 0.8180 (p) cc_final: 0.7884 (p) REVERT: C 766 ASN cc_start: 0.7577 (m-40) cc_final: 0.7140 (m-40) REVERT: C 836 LYS cc_start: 0.8111 (mppt) cc_final: 0.7675 (mmtp) REVERT: C 837 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6767 (mm-30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1861 time to fit residues: 54.4862 Evaluate side-chains 198 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 766 ASN C 809 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104965 restraints weight = 10889.119| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.43 r_work: 0.3229 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7607 Z= 0.144 Angle : 0.732 14.906 10356 Z= 0.335 Chirality : 0.049 0.214 1253 Planarity : 0.004 0.039 1270 Dihedral : 14.687 108.104 1577 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.62 % Allowed : 10.31 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.27), residues: 889 helix: -2.47 (0.41), residues: 139 sheet: -2.63 (0.38), residues: 181 loop : -1.52 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.013 0.002 PHE C 614 TYR 0.012 0.002 TYR C 582 ARG 0.002 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 16) link_NAG-ASN : angle 3.38976 ( 48) link_ALPHA1-6 : bond 0.00346 ( 3) link_ALPHA1-6 : angle 1.85241 ( 9) link_BETA1-4 : bond 0.00460 ( 8) link_BETA1-4 : angle 1.98421 ( 24) link_ALPHA1-2 : bond 0.00148 ( 1) link_ALPHA1-2 : angle 2.49283 ( 3) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 2.19104 ( 9) hydrogen bonds : bond 0.04221 ( 104) hydrogen bonds : angle 5.25580 ( 180) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.40538 ( 8) covalent geometry : bond 0.00325 ( 7572) covalent geometry : angle 0.68328 (10255) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 TRP cc_start: 0.7697 (m100) cc_final: 0.7444 (m100) REVERT: C 83 ASP cc_start: 0.7926 (p0) cc_final: 0.7640 (p0) REVERT: C 112 GLU cc_start: 0.7967 (tp30) cc_final: 0.7630 (tp30) REVERT: C 121 VAL cc_start: 0.8169 (m) cc_final: 0.7798 (t) REVERT: C 262 PHE cc_start: 0.8193 (m-80) cc_final: 0.7944 (m-80) REVERT: C 280 ILE cc_start: 0.8874 (tt) cc_final: 0.8545 (tp) REVERT: C 281 ASP cc_start: 0.8110 (t0) cc_final: 0.7895 (t0) REVERT: C 319 ASP cc_start: 0.7424 (t0) cc_final: 0.7076 (t70) REVERT: C 393 LEU cc_start: 0.8393 (tp) cc_final: 0.8134 (tt) REVERT: C 394 ASP cc_start: 0.7641 (t0) cc_final: 0.7265 (t0) REVERT: C 454 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8096 (mtm) REVERT: C 629 SER cc_start: 0.8489 (t) cc_final: 0.8106 (m) REVERT: C 773 GLN cc_start: 0.7494 (mp10) cc_final: 0.7281 (mp10) REVERT: C 836 LYS cc_start: 0.8212 (mppt) cc_final: 0.7793 (mmtp) REVERT: C 837 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7338 (mm-30) REVERT: C 881 MET cc_start: 0.7828 (tmm) cc_final: 0.7443 (tmm) outliers start: 5 outliers final: 4 residues processed: 212 average time/residue: 0.1915 time to fit residues: 54.6416 Evaluate side-chains 201 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105220 restraints weight = 11051.609| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.47 r_work: 0.3230 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7607 Z= 0.119 Angle : 0.674 14.152 10356 Z= 0.312 Chirality : 0.047 0.247 1253 Planarity : 0.004 0.038 1270 Dihedral : 12.235 111.906 1577 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.27), residues: 889 helix: -2.43 (0.41), residues: 139 sheet: -2.67 (0.38), residues: 181 loop : -1.48 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.014 0.001 PHE C 614 TYR 0.010 0.001 TYR C 256 ARG 0.003 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 16) link_NAG-ASN : angle 3.11316 ( 48) link_ALPHA1-6 : bond 0.00476 ( 3) link_ALPHA1-6 : angle 1.71836 ( 9) link_BETA1-4 : bond 0.00534 ( 8) link_BETA1-4 : angle 1.77633 ( 24) link_ALPHA1-2 : bond 0.00095 ( 1) link_ALPHA1-2 : angle 2.36958 ( 3) link_ALPHA1-3 : bond 0.00981 ( 3) link_ALPHA1-3 : angle 1.77530 ( 9) hydrogen bonds : bond 0.03634 ( 104) hydrogen bonds : angle 5.00838 ( 180) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.12333 ( 8) covalent geometry : bond 0.00263 ( 7572) covalent geometry : angle 0.63061 (10255) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7568 (t0) cc_final: 0.7330 (t0) REVERT: C 67 TRP cc_start: 0.7720 (m100) cc_final: 0.7344 (m100) REVERT: C 74 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8299 (mmmm) REVERT: C 83 ASP cc_start: 0.7897 (p0) cc_final: 0.7577 (p0) REVERT: C 112 GLU cc_start: 0.7941 (tp30) cc_final: 0.7631 (tp30) REVERT: C 182 SER cc_start: 0.8891 (t) cc_final: 0.8491 (p) REVERT: C 274 ASN cc_start: 0.8247 (m-40) cc_final: 0.8031 (m-40) REVERT: C 280 ILE cc_start: 0.8862 (tt) cc_final: 0.8537 (tp) REVERT: C 281 ASP cc_start: 0.8131 (t0) cc_final: 0.7902 (t0) REVERT: C 507 PHE cc_start: 0.8089 (p90) cc_final: 0.7863 (p90) REVERT: C 629 SER cc_start: 0.8464 (t) cc_final: 0.8129 (m) REVERT: C 773 GLN cc_start: 0.7498 (mp10) cc_final: 0.7194 (mp10) REVERT: C 836 LYS cc_start: 0.8144 (mppt) cc_final: 0.7725 (mmtp) REVERT: C 837 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7284 (mm-30) outliers start: 14 outliers final: 6 residues processed: 206 average time/residue: 0.1834 time to fit residues: 51.2762 Evaluate side-chains 199 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 193 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 327 GLN C 510 GLN C 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105269 restraints weight = 11006.098| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.46 r_work: 0.3226 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7607 Z= 0.126 Angle : 0.715 22.431 10356 Z= 0.323 Chirality : 0.049 0.380 1253 Planarity : 0.003 0.037 1270 Dihedral : 10.525 105.261 1577 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.86 % Allowed : 15.90 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.28), residues: 889 helix: -2.42 (0.42), residues: 139 sheet: -2.65 (0.38), residues: 181 loop : -1.44 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.014 0.001 PHE C 768 TYR 0.010 0.001 TYR C 658 ARG 0.002 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 16) link_NAG-ASN : angle 5.09090 ( 48) link_ALPHA1-6 : bond 0.00492 ( 3) link_ALPHA1-6 : angle 1.73387 ( 9) link_BETA1-4 : bond 0.00476 ( 8) link_BETA1-4 : angle 1.81430 ( 24) link_ALPHA1-2 : bond 0.00068 ( 1) link_ALPHA1-2 : angle 2.33368 ( 3) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 1.84636 ( 9) hydrogen bonds : bond 0.03255 ( 104) hydrogen bonds : angle 4.80051 ( 180) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.02259 ( 8) covalent geometry : bond 0.00281 ( 7572) covalent geometry : angle 0.61563 (10255) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7608 (t0) cc_final: 0.7354 (t0) REVERT: C 67 TRP cc_start: 0.7758 (m-10) cc_final: 0.7273 (m100) REVERT: C 74 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8299 (mmmm) REVERT: C 83 ASP cc_start: 0.7882 (p0) cc_final: 0.7577 (p0) REVERT: C 112 GLU cc_start: 0.7987 (tp30) cc_final: 0.7636 (tp30) REVERT: C 121 VAL cc_start: 0.8046 (m) cc_final: 0.7759 (t) REVERT: C 182 SER cc_start: 0.8909 (t) cc_final: 0.8512 (p) REVERT: C 261 ASN cc_start: 0.7063 (t0) cc_final: 0.6810 (t0) REVERT: C 263 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8361 (m) REVERT: C 281 ASP cc_start: 0.8155 (t0) cc_final: 0.7935 (t0) REVERT: C 319 ASP cc_start: 0.7488 (t0) cc_final: 0.7116 (t70) REVERT: C 507 PHE cc_start: 0.8034 (p90) cc_final: 0.7705 (p90) REVERT: C 629 SER cc_start: 0.8467 (t) cc_final: 0.8150 (m) REVERT: C 683 ASN cc_start: 0.7336 (m-40) cc_final: 0.7100 (m-40) REVERT: C 773 GLN cc_start: 0.7514 (mp10) cc_final: 0.7179 (mp10) REVERT: C 836 LYS cc_start: 0.8132 (mppt) cc_final: 0.7713 (mmtp) REVERT: C 837 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7213 (mm-30) outliers start: 15 outliers final: 9 residues processed: 207 average time/residue: 0.1926 time to fit residues: 54.2342 Evaluate side-chains 205 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 755 ASN C 876 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105939 restraints weight = 10897.662| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.46 r_work: 0.3237 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7607 Z= 0.103 Angle : 0.653 15.552 10356 Z= 0.301 Chirality : 0.046 0.275 1253 Planarity : 0.003 0.036 1270 Dihedral : 9.690 91.837 1577 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.74 % Allowed : 18.14 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.27), residues: 889 helix: -2.35 (0.42), residues: 137 sheet: -2.39 (0.45), residues: 130 loop : -1.70 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 67 HIS 0.004 0.001 HIS C 609 PHE 0.013 0.001 PHE C 768 TYR 0.008 0.001 TYR C 170 ARG 0.001 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 16) link_NAG-ASN : angle 3.98752 ( 48) link_ALPHA1-6 : bond 0.00585 ( 3) link_ALPHA1-6 : angle 1.68667 ( 9) link_BETA1-4 : bond 0.00499 ( 8) link_BETA1-4 : angle 1.85695 ( 24) link_ALPHA1-2 : bond 0.00160 ( 1) link_ALPHA1-2 : angle 2.17931 ( 3) link_ALPHA1-3 : bond 0.01103 ( 3) link_ALPHA1-3 : angle 1.84431 ( 9) hydrogen bonds : bond 0.02899 ( 104) hydrogen bonds : angle 4.64878 ( 180) SS BOND : bond 0.00271 ( 4) SS BOND : angle 1.01409 ( 8) covalent geometry : bond 0.00228 ( 7572) covalent geometry : angle 0.58314 (10255) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7612 (t0) cc_final: 0.7355 (t0) REVERT: C 83 ASP cc_start: 0.7868 (p0) cc_final: 0.7570 (p0) REVERT: C 112 GLU cc_start: 0.7963 (tp30) cc_final: 0.7646 (tp30) REVERT: C 121 VAL cc_start: 0.7950 (m) cc_final: 0.7650 (t) REVERT: C 182 SER cc_start: 0.8877 (t) cc_final: 0.8491 (p) REVERT: C 239 SER cc_start: 0.8170 (p) cc_final: 0.7940 (p) REVERT: C 246 CYS cc_start: 0.8246 (p) cc_final: 0.7985 (p) REVERT: C 261 ASN cc_start: 0.7005 (t0) cc_final: 0.6691 (t0) REVERT: C 281 ASP cc_start: 0.8162 (t0) cc_final: 0.7918 (t0) REVERT: C 629 SER cc_start: 0.8445 (t) cc_final: 0.8152 (m) REVERT: C 773 GLN cc_start: 0.7568 (mp10) cc_final: 0.7196 (mp10) REVERT: C 836 LYS cc_start: 0.8093 (mppt) cc_final: 0.7665 (mmtp) REVERT: C 837 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7221 (mm-30) outliers start: 14 outliers final: 11 residues processed: 209 average time/residue: 0.2065 time to fit residues: 59.7548 Evaluate side-chains 205 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101481 restraints weight = 11066.791| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.46 r_work: 0.3170 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.007 0.048 7607 Z= 0.309 Angle : 0.784 13.475 10356 Z= 0.368 Chirality : 0.053 0.258 1253 Planarity : 0.004 0.038 1270 Dihedral : 9.991 86.821 1577 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.61 % Allowed : 18.76 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.27), residues: 889 helix: -2.50 (0.40), residues: 146 sheet: -2.44 (0.44), residues: 135 loop : -1.92 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 67 HIS 0.006 0.002 HIS C 417 PHE 0.022 0.003 PHE C 768 TYR 0.023 0.003 TYR C 256 ARG 0.003 0.000 ARG C 794 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 16) link_NAG-ASN : angle 3.64572 ( 48) link_ALPHA1-6 : bond 0.00365 ( 3) link_ALPHA1-6 : angle 1.90551 ( 9) link_BETA1-4 : bond 0.00425 ( 8) link_BETA1-4 : angle 2.41759 ( 24) link_ALPHA1-2 : bond 0.00318 ( 1) link_ALPHA1-2 : angle 3.06697 ( 3) link_ALPHA1-3 : bond 0.00863 ( 3) link_ALPHA1-3 : angle 1.81587 ( 9) hydrogen bonds : bond 0.04346 ( 104) hydrogen bonds : angle 5.13014 ( 180) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.40658 ( 8) covalent geometry : bond 0.00701 ( 7572) covalent geometry : angle 0.73060 (10255) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7672 (t0) cc_final: 0.7436 (t0) REVERT: C 83 ASP cc_start: 0.7870 (p0) cc_final: 0.7594 (p0) REVERT: C 112 GLU cc_start: 0.7976 (tp30) cc_final: 0.7619 (tp30) REVERT: C 131 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8442 (mtp85) REVERT: C 182 SER cc_start: 0.8969 (t) cc_final: 0.8575 (p) REVERT: C 261 ASN cc_start: 0.7078 (t0) cc_final: 0.6739 (t0) REVERT: C 281 ASP cc_start: 0.8167 (t0) cc_final: 0.7953 (t0) REVERT: C 319 ASP cc_start: 0.7544 (t0) cc_final: 0.7159 (t70) REVERT: C 394 ASP cc_start: 0.7636 (t0) cc_final: 0.7277 (t0) REVERT: C 629 SER cc_start: 0.8413 (t) cc_final: 0.8192 (m) REVERT: C 683 ASN cc_start: 0.7639 (m-40) cc_final: 0.7361 (m-40) REVERT: C 773 GLN cc_start: 0.7674 (mp10) cc_final: 0.7149 (mp10) REVERT: C 836 LYS cc_start: 0.8257 (mppt) cc_final: 0.7826 (mmtp) REVERT: C 837 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7363 (mm-30) REVERT: C 838 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6732 (mmt) outliers start: 21 outliers final: 13 residues processed: 213 average time/residue: 0.1937 time to fit residues: 55.4027 Evaluate side-chains 214 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 838 MET Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN C 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104278 restraints weight = 10897.126| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.44 r_work: 0.3211 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7607 Z= 0.121 Angle : 0.676 13.806 10356 Z= 0.317 Chirality : 0.047 0.280 1253 Planarity : 0.003 0.036 1270 Dihedral : 9.402 82.705 1577 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.36 % Allowed : 19.50 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.27), residues: 889 helix: -2.43 (0.41), residues: 146 sheet: -2.45 (0.45), residues: 130 loop : -1.82 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 715 HIS 0.004 0.001 HIS C 609 PHE 0.017 0.001 PHE C 768 TYR 0.020 0.002 TYR C 920 ARG 0.002 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 16) link_NAG-ASN : angle 3.31730 ( 48) link_ALPHA1-6 : bond 0.00590 ( 3) link_ALPHA1-6 : angle 1.68109 ( 9) link_BETA1-4 : bond 0.00446 ( 8) link_BETA1-4 : angle 1.98912 ( 24) link_ALPHA1-2 : bond 0.00226 ( 1) link_ALPHA1-2 : angle 2.46772 ( 3) link_ALPHA1-3 : bond 0.01028 ( 3) link_ALPHA1-3 : angle 1.76377 ( 9) hydrogen bonds : bond 0.03190 ( 104) hydrogen bonds : angle 4.82854 ( 180) SS BOND : bond 0.00267 ( 4) SS BOND : angle 1.29762 ( 8) covalent geometry : bond 0.00271 ( 7572) covalent geometry : angle 0.62642 (10255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7634 (t0) cc_final: 0.7402 (t0) REVERT: C 83 ASP cc_start: 0.7800 (p0) cc_final: 0.7549 (p0) REVERT: C 112 GLU cc_start: 0.7925 (tp30) cc_final: 0.7580 (tp30) REVERT: C 182 SER cc_start: 0.8971 (t) cc_final: 0.8584 (p) REVERT: C 261 ASN cc_start: 0.7023 (t0) cc_final: 0.6599 (t0) REVERT: C 274 ASN cc_start: 0.8140 (m-40) cc_final: 0.7927 (m-40) REVERT: C 281 ASP cc_start: 0.8117 (t0) cc_final: 0.7873 (t0) REVERT: C 629 SER cc_start: 0.8436 (t) cc_final: 0.8186 (m) REVERT: C 683 ASN cc_start: 0.7551 (m-40) cc_final: 0.7246 (m-40) REVERT: C 773 GLN cc_start: 0.7623 (mp10) cc_final: 0.7046 (mp10) REVERT: C 836 LYS cc_start: 0.8157 (mppt) cc_final: 0.7738 (mmtp) REVERT: C 837 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7295 (mm-30) REVERT: C 838 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6483 (mmt) outliers start: 19 outliers final: 11 residues processed: 212 average time/residue: 0.1931 time to fit residues: 55.3939 Evaluate side-chains 210 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 838 MET Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN C 755 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104658 restraints weight = 11096.563| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.48 r_work: 0.3216 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7607 Z= 0.115 Angle : 0.668 13.680 10356 Z= 0.313 Chirality : 0.046 0.280 1253 Planarity : 0.003 0.036 1270 Dihedral : 9.060 79.721 1577 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.86 % Allowed : 20.37 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.28), residues: 889 helix: -2.44 (0.41), residues: 147 sheet: -2.67 (0.37), residues: 187 loop : -1.43 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 67 HIS 0.004 0.001 HIS C 609 PHE 0.018 0.001 PHE C 614 TYR 0.015 0.001 TYR C 920 ARG 0.001 0.000 ARG C 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 16) link_NAG-ASN : angle 3.15894 ( 48) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 1.66009 ( 9) link_BETA1-4 : bond 0.00482 ( 8) link_BETA1-4 : angle 1.96522 ( 24) link_ALPHA1-2 : bond 0.00182 ( 1) link_ALPHA1-2 : angle 2.32705 ( 3) link_ALPHA1-3 : bond 0.01035 ( 3) link_ALPHA1-3 : angle 1.75557 ( 9) hydrogen bonds : bond 0.03018 ( 104) hydrogen bonds : angle 4.77604 ( 180) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.23017 ( 8) covalent geometry : bond 0.00260 ( 7572) covalent geometry : angle 0.62235 (10255) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7815 (p0) cc_final: 0.7556 (p0) REVERT: C 112 GLU cc_start: 0.7929 (tp30) cc_final: 0.7589 (tp30) REVERT: C 182 SER cc_start: 0.8938 (t) cc_final: 0.8549 (p) REVERT: C 281 ASP cc_start: 0.8130 (t0) cc_final: 0.7890 (t0) REVERT: C 629 SER cc_start: 0.8424 (t) cc_final: 0.8182 (m) REVERT: C 640 GLU cc_start: 0.8104 (mp0) cc_final: 0.7882 (mp0) REVERT: C 683 ASN cc_start: 0.7574 (m-40) cc_final: 0.7259 (m-40) REVERT: C 773 GLN cc_start: 0.7575 (mp10) cc_final: 0.7067 (mp10) REVERT: C 836 LYS cc_start: 0.8136 (mppt) cc_final: 0.7710 (mmtp) REVERT: C 837 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7294 (mm-30) REVERT: C 838 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6437 (mmt) outliers start: 15 outliers final: 12 residues processed: 207 average time/residue: 0.1918 time to fit residues: 54.1613 Evaluate side-chains 211 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 838 MET Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 755 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102406 restraints weight = 11112.900| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.47 r_work: 0.3174 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7607 Z= 0.232 Angle : 0.743 13.681 10356 Z= 0.349 Chirality : 0.050 0.256 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.257 79.735 1577 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.36 % Allowed : 20.37 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.27), residues: 889 helix: -2.38 (0.42), residues: 138 sheet: -2.55 (0.42), residues: 149 loop : -1.83 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 67 HIS 0.005 0.002 HIS C 417 PHE 0.017 0.002 PHE C 410 TYR 0.022 0.002 TYR C 920 ARG 0.002 0.000 ARG C 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 16) link_NAG-ASN : angle 3.20161 ( 48) link_ALPHA1-6 : bond 0.00405 ( 3) link_ALPHA1-6 : angle 1.76260 ( 9) link_BETA1-4 : bond 0.00429 ( 8) link_BETA1-4 : angle 2.28073 ( 24) link_ALPHA1-2 : bond 0.00324 ( 1) link_ALPHA1-2 : angle 2.78210 ( 3) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.78598 ( 9) hydrogen bonds : bond 0.03753 ( 104) hydrogen bonds : angle 4.90130 ( 180) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.42772 ( 8) covalent geometry : bond 0.00529 ( 7572) covalent geometry : angle 0.69824 (10255) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7826 (p0) cc_final: 0.7564 (p0) REVERT: C 112 GLU cc_start: 0.7931 (tp30) cc_final: 0.7580 (tp30) REVERT: C 182 SER cc_start: 0.8939 (t) cc_final: 0.8544 (p) REVERT: C 274 ASN cc_start: 0.8162 (m-40) cc_final: 0.7954 (m-40) REVERT: C 281 ASP cc_start: 0.8162 (t0) cc_final: 0.7910 (t0) REVERT: C 500 SER cc_start: 0.8501 (t) cc_final: 0.8263 (p) REVERT: C 629 SER cc_start: 0.8408 (t) cc_final: 0.8171 (m) REVERT: C 640 GLU cc_start: 0.8218 (mp0) cc_final: 0.8005 (mp0) REVERT: C 683 ASN cc_start: 0.7591 (m-40) cc_final: 0.7289 (m-40) REVERT: C 773 GLN cc_start: 0.7648 (mp10) cc_final: 0.7110 (mp10) REVERT: C 836 LYS cc_start: 0.8229 (mppt) cc_final: 0.7814 (mmtp) REVERT: C 837 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 838 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: C 882 ILE cc_start: 0.7900 (tp) cc_final: 0.7695 (tt) outliers start: 19 outliers final: 13 residues processed: 213 average time/residue: 0.1920 time to fit residues: 55.4608 Evaluate side-chains 214 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 838 MET Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN C 198 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.104927 restraints weight = 11009.677| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.46 r_work: 0.3223 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7607 Z= 0.114 Angle : 0.682 13.821 10356 Z= 0.320 Chirality : 0.047 0.287 1253 Planarity : 0.003 0.036 1270 Dihedral : 8.708 77.577 1577 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.86 % Allowed : 21.12 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.27), residues: 889 helix: -2.28 (0.44), residues: 131 sheet: -2.53 (0.43), residues: 139 loop : -1.75 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 715 HIS 0.004 0.001 HIS C 609 PHE 0.016 0.001 PHE C 768 TYR 0.015 0.001 TYR C 920 ARG 0.002 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 16) link_NAG-ASN : angle 3.04936 ( 48) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.62402 ( 9) link_BETA1-4 : bond 0.00495 ( 8) link_BETA1-4 : angle 1.95178 ( 24) link_ALPHA1-2 : bond 0.00070 ( 1) link_ALPHA1-2 : angle 2.24943 ( 3) link_ALPHA1-3 : bond 0.01027 ( 3) link_ALPHA1-3 : angle 1.70614 ( 9) hydrogen bonds : bond 0.02934 ( 104) hydrogen bonds : angle 4.55343 ( 180) SS BOND : bond 0.00167 ( 4) SS BOND : angle 1.24412 ( 8) covalent geometry : bond 0.00254 ( 7572) covalent geometry : angle 0.64011 (10255) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7761 (p0) cc_final: 0.7541 (p0) REVERT: C 112 GLU cc_start: 0.7931 (tp30) cc_final: 0.7562 (tp30) REVERT: C 182 SER cc_start: 0.8919 (t) cc_final: 0.8525 (p) REVERT: C 500 SER cc_start: 0.8534 (t) cc_final: 0.8293 (p) REVERT: C 629 SER cc_start: 0.8388 (t) cc_final: 0.8144 (m) REVERT: C 768 PHE cc_start: 0.8596 (m-80) cc_final: 0.7953 (m-80) REVERT: C 773 GLN cc_start: 0.7611 (mp10) cc_final: 0.7037 (mp10) REVERT: C 836 LYS cc_start: 0.8159 (mppt) cc_final: 0.7722 (mmtp) REVERT: C 837 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7302 (mm-30) REVERT: C 838 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6433 (mmt) outliers start: 15 outliers final: 12 residues processed: 212 average time/residue: 0.1854 time to fit residues: 53.6139 Evaluate side-chains 215 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 838 MET Chi-restraints excluded: chain C residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 70 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102773 restraints weight = 10986.214| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.48 r_work: 0.3191 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7607 Z= 0.201 Angle : 0.727 13.719 10356 Z= 0.342 Chirality : 0.049 0.248 1253 Planarity : 0.004 0.036 1270 Dihedral : 8.831 77.519 1577 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 1.86 % Allowed : 21.61 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.27), residues: 889 helix: -2.32 (0.43), residues: 132 sheet: -2.66 (0.40), residues: 159 loop : -1.73 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 715 HIS 0.005 0.002 HIS C 417 PHE 0.018 0.002 PHE C 768 TYR 0.018 0.002 TYR C 920 ARG 0.002 0.000 ARG C 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 16) link_NAG-ASN : angle 3.07317 ( 48) link_ALPHA1-6 : bond 0.00463 ( 3) link_ALPHA1-6 : angle 1.69914 ( 9) link_BETA1-4 : bond 0.00469 ( 8) link_BETA1-4 : angle 2.22810 ( 24) link_ALPHA1-2 : bond 0.00291 ( 1) link_ALPHA1-2 : angle 2.61945 ( 3) link_ALPHA1-3 : bond 0.00992 ( 3) link_ALPHA1-3 : angle 1.72786 ( 9) hydrogen bonds : bond 0.03548 ( 104) hydrogen bonds : angle 4.75673 ( 180) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.38877 ( 8) covalent geometry : bond 0.00458 ( 7572) covalent geometry : angle 0.68479 (10255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.09 seconds wall clock time: 80 minutes 38.93 seconds (4838.93 seconds total)