Starting phenix.real_space_refine on Tue Sep 24 08:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_32295.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_32295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_32295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_32295.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/09_2024/7w3x_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-5461/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: 4.94, 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: 2.50 Conformation dependent library (CDL) restraints added in 889.1 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: 1.07 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: 2.82 Time building geometry restraints manager: 2.81 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- 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 7572 Z= 0.271 Angle : 0.765 8.124 10255 Z= 0.366 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.069 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: 0.2115 time to fit residues: 62.4834 Evaluate side-chains 198 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7572 Z= 0.244 Angle : 0.693 8.739 10255 Z= 0.330 Chirality : 0.049 0.214 1253 Planarity : 0.004 0.040 1270 Dihedral : 14.924 108.246 1577 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % 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: -2.90 (0.27), residues: 889 helix: -2.47 (0.41), residues: 139 sheet: -2.64 (0.37), residues: 181 loop : -1.54 (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 0.012 0.002 PHE C 768 TYR 0.013 0.002 TYR C 582 ARG 0.002 0.000 ARG C 131 *********************** 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 215 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 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 67 TRP cc_start: 0.7493 (m100) cc_final: 0.7273 (m100) REVERT: C 83 ASP cc_start: 0.7317 (p0) cc_final: 0.7032 (p0) REVERT: C 112 GLU cc_start: 0.7382 (tp30) cc_final: 0.7099 (tp30) REVERT: C 121 VAL cc_start: 0.7866 (m) cc_final: 0.7556 (t) REVERT: C 262 PHE cc_start: 0.8129 (m-80) cc_final: 0.7843 (m-80) REVERT: C 280 ILE cc_start: 0.8848 (tt) cc_final: 0.8528 (tp) REVERT: C 319 ASP cc_start: 0.6791 (t0) cc_final: 0.6405 (t70) REVERT: C 394 ASP cc_start: 0.6974 (t0) cc_final: 0.6650 (t0) REVERT: C 418 LEU cc_start: 0.8138 (mt) cc_final: 0.7858 (mp) REVERT: C 454 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: C 629 SER cc_start: 0.8278 (t) cc_final: 0.7910 (m) REVERT: C 668 SER cc_start: 0.8196 (p) cc_final: 0.7892 (p) REVERT: C 836 LYS cc_start: 0.8063 (mppt) cc_final: 0.7641 (mmtp) REVERT: C 837 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6787 (mm-30) REVERT: C 881 MET cc_start: 0.7658 (tmm) cc_final: 0.7274 (tmm) outliers start: 5 outliers final: 4 residues processed: 211 average time/residue: 0.1976 time to fit residues: 55.8016 Evaluate side-chains 200 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7572 Z= 0.191 Angle : 0.645 9.568 10255 Z= 0.308 Chirality : 0.047 0.247 1253 Planarity : 0.004 0.038 1270 Dihedral : 12.165 112.356 1577 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.61 % Allowed : 13.91 % Favored : 84.47 % 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: -2.43 (0.41), residues: 139 sheet: -2.68 (0.38), residues: 181 loop : -1.51 (0.25), 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 0.013 0.001 PHE C 685 TYR 0.011 0.001 TYR C 789 ARG 0.003 0.000 ARG C 131 *********************** 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 fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 ASP cc_start: 0.7194 (t0) cc_final: 0.6988 (t0) REVERT: C 67 TRP cc_start: 0.7507 (m100) cc_final: 0.7131 (m100) REVERT: C 83 ASP cc_start: 0.7276 (p0) cc_final: 0.6961 (p0) REVERT: C 112 GLU cc_start: 0.7381 (tp30) cc_final: 0.7120 (tp30) REVERT: C 182 SER cc_start: 0.8798 (t) cc_final: 0.8425 (p) REVERT: C 280 ILE cc_start: 0.8830 (tt) cc_final: 0.8519 (tp) REVERT: C 319 ASP cc_start: 0.6791 (t0) cc_final: 0.6397 (t70) REVERT: C 507 PHE cc_start: 0.7899 (p90) cc_final: 0.7673 (p90) REVERT: C 629 SER cc_start: 0.8257 (t) cc_final: 0.7933 (m) REVERT: C 668 SER cc_start: 0.8127 (p) cc_final: 0.7872 (p) REVERT: C 773 GLN cc_start: 0.7254 (mp10) cc_final: 0.6961 (mp10) REVERT: C 836 LYS cc_start: 0.8015 (mppt) cc_final: 0.7587 (mmtp) REVERT: C 837 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6715 (mm-30) outliers start: 13 outliers final: 5 residues processed: 207 average time/residue: 0.1857 time to fit residues: 52.1870 Evaluate side-chains 201 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 C 510 GLN C 755 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7572 Z= 0.254 Angle : 0.643 8.264 10255 Z= 0.312 Chirality : 0.049 0.263 1253 Planarity : 0.004 0.037 1270 Dihedral : 10.440 102.353 1577 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.11 % Allowed : 16.15 % Favored : 81.74 % 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: -2.90 (0.27), residues: 889 helix: -2.40 (0.42), residues: 139 sheet: -2.70 (0.37), residues: 186 loop : -1.52 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.016 0.002 PHE C 768 TYR 0.015 0.002 TYR C 789 ARG 0.002 0.000 ARG C 131 *********************** 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 219 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7208 (p0) cc_final: 0.6917 (p0) REVERT: C 112 GLU cc_start: 0.7385 (tp30) cc_final: 0.7101 (tp30) REVERT: C 182 SER cc_start: 0.8827 (t) cc_final: 0.8462 (p) REVERT: C 280 ILE cc_start: 0.8845 (tt) cc_final: 0.8539 (tp) REVERT: C 319 ASP cc_start: 0.6810 (t0) cc_final: 0.6417 (t70) REVERT: C 507 PHE cc_start: 0.7817 (p90) cc_final: 0.7607 (p90) REVERT: C 629 SER cc_start: 0.8231 (t) cc_final: 0.7957 (m) REVERT: C 668 SER cc_start: 0.8128 (p) cc_final: 0.7884 (p) REVERT: C 683 ASN cc_start: 0.7170 (m-40) cc_final: 0.6903 (m-40) REVERT: C 773 GLN cc_start: 0.7284 (mp10) cc_final: 0.6935 (mp10) REVERT: C 836 LYS cc_start: 0.8018 (mppt) cc_final: 0.7592 (mmtp) REVERT: C 837 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6728 (mm-30) REVERT: C 920 TYR cc_start: 0.8450 (m-80) cc_final: 0.8231 (m-80) outliers start: 17 outliers final: 11 residues processed: 212 average time/residue: 0.1831 time to fit residues: 52.7727 Evaluate side-chains 201 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 309 PHE 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 605 ILE Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 844 LEU 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 1 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 510 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN C 876 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7572 Z= 0.279 Angle : 0.647 9.812 10255 Z= 0.317 Chirality : 0.049 0.270 1253 Planarity : 0.004 0.037 1270 Dihedral : 9.980 90.826 1577 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.48 % Allowed : 17.89 % Favored : 79.63 % 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: -3.02 (0.27), residues: 889 helix: -2.44 (0.41), residues: 146 sheet: -2.44 (0.44), residues: 135 loop : -1.87 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.019 0.002 PHE C 768 TYR 0.015 0.002 TYR C 789 ARG 0.002 0.000 ARG C 794 *********************** 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 220 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 0.878 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 74 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8281 (mmmm) REVERT: C 83 ASP cc_start: 0.7182 (p0) cc_final: 0.6893 (p0) REVERT: C 112 GLU cc_start: 0.7360 (tp30) cc_final: 0.7100 (tp30) REVERT: C 182 SER cc_start: 0.8850 (t) cc_final: 0.8497 (p) REVERT: C 319 ASP cc_start: 0.6838 (t0) cc_final: 0.6417 (t70) REVERT: C 507 PHE cc_start: 0.7818 (p90) cc_final: 0.7611 (p90) REVERT: C 629 SER cc_start: 0.8219 (t) cc_final: 0.7957 (m) REVERT: C 668 SER cc_start: 0.8139 (p) cc_final: 0.7879 (p) REVERT: C 683 ASN cc_start: 0.7092 (m-40) cc_final: 0.6856 (m-40) REVERT: C 773 GLN cc_start: 0.7336 (mp10) cc_final: 0.6908 (mp10) REVERT: C 836 LYS cc_start: 0.8013 (mppt) cc_final: 0.7599 (mmtp) REVERT: C 837 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6712 (mm-30) REVERT: C 920 TYR cc_start: 0.8449 (m-80) cc_final: 0.8241 (m-80) outliers start: 20 outliers final: 16 residues processed: 209 average time/residue: 0.1875 time to fit residues: 52.8781 Evaluate side-chains 210 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 226 VAL 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 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 797 SER Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 LEU 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 50 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 510 GLN C 513 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7572 Z= 0.232 Angle : 0.631 8.958 10255 Z= 0.309 Chirality : 0.048 0.277 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.596 85.838 1577 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.36 % Allowed : 19.01 % 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: -3.02 (0.27), residues: 889 helix: -2.45 (0.41), residues: 146 sheet: -2.43 (0.45), residues: 130 loop : -1.87 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 715 HIS 0.005 0.001 HIS C 609 PHE 0.018 0.002 PHE C 768 TYR 0.013 0.002 TYR C 789 ARG 0.001 0.000 ARG C 131 *********************** 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 219 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.885 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 74 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8271 (mmmm) REVERT: C 83 ASP cc_start: 0.7163 (p0) cc_final: 0.6896 (p0) REVERT: C 112 GLU cc_start: 0.7352 (tp30) cc_final: 0.7067 (tp30) REVERT: C 182 SER cc_start: 0.8809 (t) cc_final: 0.8473 (p) REVERT: C 239 SER cc_start: 0.8043 (p) cc_final: 0.7792 (p) REVERT: C 240 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 319 ASP cc_start: 0.6829 (t0) cc_final: 0.6411 (t70) REVERT: C 629 SER cc_start: 0.8221 (t) cc_final: 0.7959 (m) REVERT: C 668 SER cc_start: 0.8116 (p) cc_final: 0.7868 (p) REVERT: C 773 GLN cc_start: 0.7329 (mp10) cc_final: 0.6861 (mp10) REVERT: C 836 LYS cc_start: 0.8000 (mppt) cc_final: 0.7585 (mmtp) REVERT: C 837 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6768 (mm-30) REVERT: C 838 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6141 (mmt) REVERT: C 920 TYR cc_start: 0.8447 (m-80) cc_final: 0.8234 (m-80) outliers start: 19 outliers final: 14 residues processed: 208 average time/residue: 0.1876 time to fit residues: 52.7192 Evaluate side-chains 209 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 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 437 LEU 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 797 SER 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 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7572 Z= 0.200 Angle : 0.654 11.200 10255 Z= 0.314 Chirality : 0.061 1.251 1253 Planarity : 0.004 0.035 1270 Dihedral : 9.471 82.599 1577 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.73 % Allowed : 19.13 % 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: -2.88 (0.28), residues: 889 helix: -2.45 (0.41), residues: 147 sheet: -2.63 (0.38), residues: 185 loop : -1.48 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 67 HIS 0.005 0.001 HIS C 609 PHE 0.016 0.001 PHE C 260 TYR 0.011 0.001 TYR C 256 ARG 0.001 0.000 ARG C 724 *********************** 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 219 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 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: symmetry clash REVERT: C 83 ASP cc_start: 0.7153 (p0) cc_final: 0.6892 (p0) REVERT: C 112 GLU cc_start: 0.7341 (tp30) cc_final: 0.7060 (tp30) REVERT: C 182 SER cc_start: 0.8807 (t) cc_final: 0.8454 (p) REVERT: C 239 SER cc_start: 0.8011 (p) cc_final: 0.7758 (p) REVERT: C 240 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7221 (tt) REVERT: C 274 ASN cc_start: 0.7886 (m-40) cc_final: 0.7681 (m-40) REVERT: C 629 SER cc_start: 0.8201 (t) cc_final: 0.7945 (m) REVERT: C 668 SER cc_start: 0.8118 (p) cc_final: 0.7869 (p) REVERT: C 773 GLN cc_start: 0.7319 (mp10) cc_final: 0.6848 (mp10) REVERT: C 836 LYS cc_start: 0.7985 (mppt) cc_final: 0.7567 (mmtp) REVERT: C 837 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6748 (mm-30) REVERT: C 920 TYR cc_start: 0.8444 (m-80) cc_final: 0.8237 (m-80) outliers start: 22 outliers final: 16 residues processed: 210 average time/residue: 0.1889 time to fit residues: 54.1246 Evaluate side-chains 209 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 261 ASN 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 390 LEU 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 797 SER Chi-restraints excluded: chain C residue 834 ILE 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 16 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7572 Z= 0.346 Angle : 0.698 9.580 10255 Z= 0.344 Chirality : 0.052 0.458 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.587 80.919 1577 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.61 % Allowed : 19.25 % 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: -3.09 (0.27), residues: 889 helix: -2.48 (0.40), residues: 146 sheet: -2.49 (0.45), residues: 130 loop : -1.93 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 67 HIS 0.006 0.002 HIS C 609 PHE 0.020 0.002 PHE C 768 TYR 0.019 0.002 TYR C 789 ARG 0.003 0.000 ARG C 368 *********************** 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 223 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 0.978 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 67 TRP cc_start: 0.7895 (m-10) cc_final: 0.7082 (m100) REVERT: C 83 ASP cc_start: 0.7148 (p0) cc_final: 0.6866 (p0) REVERT: C 112 GLU cc_start: 0.7350 (tp30) cc_final: 0.7085 (tp30) REVERT: C 182 SER cc_start: 0.8797 (t) cc_final: 0.8446 (p) REVERT: C 239 SER cc_start: 0.8099 (p) cc_final: 0.7819 (p) REVERT: C 240 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7310 (tt) REVERT: C 319 ASP cc_start: 0.6742 (t0) cc_final: 0.6303 (t70) REVERT: C 629 SER cc_start: 0.8200 (t) cc_final: 0.7948 (m) REVERT: C 668 SER cc_start: 0.8142 (p) cc_final: 0.7881 (p) REVERT: C 773 GLN cc_start: 0.7373 (mp10) cc_final: 0.6809 (mp10) REVERT: C 836 LYS cc_start: 0.8092 (mppt) cc_final: 0.7670 (mmtp) REVERT: C 837 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 920 TYR cc_start: 0.8460 (m-80) cc_final: 0.8251 (m-80) outliers start: 21 outliers final: 14 residues processed: 212 average time/residue: 0.1856 time to fit residues: 53.1849 Evaluate side-chains 209 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 240 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 390 LEU Chi-restraints excluded: chain C residue 489 ASP 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 834 ILE 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 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 351 ASN C 508 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN C 755 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7572 Z= 0.282 Angle : 0.678 8.671 10255 Z= 0.332 Chirality : 0.049 0.256 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.324 80.632 1577 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 2.24 % Allowed : 20.00 % 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: -3.08 (0.27), residues: 889 helix: -2.48 (0.40), residues: 146 sheet: -2.50 (0.44), residues: 135 loop : -1.91 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 715 HIS 0.005 0.002 HIS C 609 PHE 0.021 0.002 PHE C 768 TYR 0.016 0.002 TYR C 789 ARG 0.002 0.000 ARG C 851 *********************** 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 217 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 TRP cc_start: 0.7866 (m-10) cc_final: 0.7546 (m100) REVERT: C 83 ASP cc_start: 0.7124 (p0) cc_final: 0.6835 (p0) REVERT: C 112 GLU cc_start: 0.7336 (tp30) cc_final: 0.7062 (tp30) REVERT: C 182 SER cc_start: 0.8783 (t) cc_final: 0.8420 (p) REVERT: C 239 SER cc_start: 0.8062 (p) cc_final: 0.7810 (p) REVERT: C 240 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7299 (tt) REVERT: C 319 ASP cc_start: 0.6761 (t0) cc_final: 0.6342 (t70) REVERT: C 351 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7412 (p0) REVERT: C 629 SER cc_start: 0.8204 (t) cc_final: 0.7947 (m) REVERT: C 765 PHE cc_start: 0.7931 (m-10) cc_final: 0.7696 (m-80) REVERT: C 773 GLN cc_start: 0.7364 (mp10) cc_final: 0.6700 (mp10) REVERT: C 836 LYS cc_start: 0.8092 (mppt) cc_final: 0.7674 (mmtp) REVERT: C 837 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 920 TYR cc_start: 0.8454 (m-80) cc_final: 0.8241 (m-80) outliers start: 18 outliers final: 15 residues processed: 207 average time/residue: 0.1844 time to fit residues: 51.7551 Evaluate side-chains 209 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 240 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 351 ASN Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 489 ASP 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 688 MET Chi-restraints excluded: chain C residue 834 ILE 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 88 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 755 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 7572 Z= 0.232 Angle : 0.692 9.812 10255 Z= 0.341 Chirality : 0.050 0.444 1253 Planarity : 0.004 0.035 1270 Dihedral : 9.164 79.737 1577 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.99 % Allowed : 20.75 % Favored : 77.27 % Cbeta Deviations : 0.12 % 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: -2.89 (0.27), residues: 889 helix: -2.25 (0.44), residues: 131 sheet: -2.48 (0.45), residues: 130 loop : -1.81 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 715 HIS 0.005 0.001 HIS C 609 PHE 0.019 0.002 PHE C 614 TYR 0.012 0.001 TYR C 256 ARG 0.002 0.000 ARG C 335 ********************** 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 217 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 TRP cc_start: 0.7898 (m-10) cc_final: 0.7245 (m100) REVERT: C 83 ASP cc_start: 0.7103 (p0) cc_final: 0.6889 (p0) REVERT: C 112 GLU cc_start: 0.7328 (tp30) cc_final: 0.7064 (tp30) REVERT: C 182 SER cc_start: 0.8779 (t) cc_final: 0.8413 (p) REVERT: C 239 SER cc_start: 0.8027 (p) cc_final: 0.7756 (p) REVERT: C 319 ASP cc_start: 0.6754 (t0) cc_final: 0.6305 (t70) REVERT: C 351 ASN cc_start: 0.7448 (p0) cc_final: 0.7232 (p0) REVERT: C 629 SER cc_start: 0.8178 (t) cc_final: 0.7921 (m) REVERT: C 773 GLN cc_start: 0.7317 (mp10) cc_final: 0.7067 (mp10) REVERT: C 836 LYS cc_start: 0.8087 (mppt) cc_final: 0.7656 (mmtp) REVERT: C 837 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6883 (mm-30) REVERT: C 920 TYR cc_start: 0.8448 (m-80) cc_final: 0.8232 (m-80) outliers start: 16 outliers final: 14 residues processed: 209 average time/residue: 0.1912 time to fit residues: 53.9798 Evaluate side-chains 210 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 437 LEU 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 688 MET Chi-restraints excluded: chain C residue 834 ILE 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 19 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.3528 r_free = 0.3528 target = 0.117626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104595 restraints weight = 10783.957| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.43 r_work: 0.3217 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7572 Z= 0.215 Angle : 0.699 9.814 10255 Z= 0.343 Chirality : 0.049 0.331 1253 Planarity : 0.004 0.035 1270 Dihedral : 10.578 113.528 1577 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.49 % Allowed : 21.24 % Favored : 77.27 % Cbeta Deviations : 0.12 % 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: -2.77 (0.28), residues: 889 helix: -2.24 (0.45), residues: 126 sheet: -2.64 (0.38), residues: 185 loop : -1.47 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP C 715 HIS 0.005 0.001 HIS C 609 PHE 0.022 0.002 PHE C 262 TYR 0.011 0.001 TYR C 256 ARG 0.004 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.07 seconds wall clock time: 40 minutes 31.65 seconds (2431.65 seconds total)