Starting phenix.real_space_refine on Tue Dec 31 09:36:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5t_21547/12_2024/6w5t_21547.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. 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 71 5.16 5 C 6156 2.51 5 N 1496 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "D" 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: "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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.28, per 1000 atoms: 0.66 Number of scatterers: 9505 At special positions: 0 Unit cell: (103.602, 91.348, 152.618, 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 71 16.00 O 1782 8.00 N 1496 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=1.51 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.06 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.97 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " 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 ALPHA1-3 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 59.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.599A pdb=" N CYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.608A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.043A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.991A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 330 through 349 removed outlier: 4.150A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.520A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.534A pdb=" N TYR A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.510A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 594 removed outlier: 3.652A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 620 through 639 removed outlier: 4.106A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 720 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 789 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.634A pdb=" N PHE A 820 " --> pdb=" O CYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.747A pdb=" N ILE A 837 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 4.029A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.983A pdb=" N ASP A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.073A pdb=" N GLN A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.400A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.720A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 removed outlier: 3.537A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1177 removed outlier: 4.007A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.301A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1219 through 1242 removed outlier: 4.526A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1252 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 127 removed outlier: 3.915A pdb=" N ASN A 122 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 145 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 1039 through 1043 Processing sheet with id=AA5, first strand: chain 'A' and resid 958 through 960 Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025 removed outlier: 5.328A pdb=" N ASN A1024 " --> pdb=" O GLY A1034 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2947 1.35 - 1.48: 2625 1.48 - 1.61: 4081 1.61 - 1.74: 1 1.74 - 1.87: 99 Bond restraints: 9753 Sorted by residual: bond pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.27e-02 6.20e+03 1.90e+01 bond pdb=" N CYS A 909 " pdb=" CA CYS A 909 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA TYR A 269 " pdb=" C TYR A 269 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.39e-02 5.18e+03 1.23e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 ... (remaining 9748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 13253 5.48 - 10.95: 38 10.95 - 16.43: 4 16.43 - 21.90: 0 21.90 - 27.38: 1 Bond angle restraints: 13296 Sorted by residual: angle pdb=" N CYS A 909 " pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 111.07 138.45 -27.38 1.07e+00 8.73e-01 6.55e+02 angle pdb=" N ASN A 823 " pdb=" CA ASN A 823 " pdb=" C ASN A 823 " ideal model delta sigma weight residual 111.14 121.36 -10.22 1.08e+00 8.57e-01 8.95e+01 angle pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" C SER A 602 " ideal model delta sigma weight residual 108.41 97.30 11.11 1.63e+00 3.76e-01 4.64e+01 angle pdb=" CA CYS A 909 " pdb=" C CYS A 909 " pdb=" N GLY A 910 " ideal model delta sigma weight residual 117.07 124.47 -7.40 1.14e+00 7.69e-01 4.21e+01 angle pdb=" C GLY A 910 " pdb=" N GLY A 911 " pdb=" CA GLY A 911 " ideal model delta sigma weight residual 122.42 129.43 -7.01 1.13e+00 7.83e-01 3.85e+01 ... (remaining 13291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 5696 27.95 - 55.90: 304 55.90 - 83.85: 53 83.85 - 111.80: 33 111.80 - 139.76: 13 Dihedral angle restraints: 6099 sinusoidal: 2677 harmonic: 3422 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 0.20 -86.20 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta harmonic sigma weight residual 180.00 -137.91 -42.09 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 1555 0.948 - 1.896: 0 1.896 - 2.844: 0 2.844 - 3.792: 0 3.792 - 4.740: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.34 -4.74 2.00e-02 2.50e+03 5.62e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.33 -4.73 2.00e-02 2.50e+03 5.59e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.38e+02 ... (remaining 1554 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG C 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.344 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG E 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.077 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 9588 3.19 - 3.76: 14483 3.76 - 4.33: 20142 4.33 - 4.90: 32725 Nonbonded interactions: 77113 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.054 3.040 nonbonded pdb=" OH TYR A 487 " pdb=" O VAL A 541 " model vdw 2.077 3.040 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.134 3.120 nonbonded pdb=" OD1 ASN A 459 " pdb=" N2 NAG A1402 " model vdw 2.200 3.120 nonbonded pdb=" N GLN A 716 " pdb=" OE1 GLN A 716 " model vdw 2.206 3.120 ... (remaining 77108 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' } ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) } 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 group one per residue 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.007 0.083 9753 Z= 0.455 Angle : 1.144 27.378 13296 Z= 0.714 Chirality : 0.182 4.740 1557 Planarity : 0.015 0.298 1664 Dihedral : 19.767 139.756 3854 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 48.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.97 % Favored : 91.52 % Rotamer: Outliers : 5.60 % Allowed : 8.95 % Favored : 85.45 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.22), residues: 1167 helix: -0.92 (0.20), residues: 591 sheet: -2.19 (0.58), residues: 87 loop : -2.97 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 27 HIS 0.004 0.001 HIS A1239 PHE 0.031 0.002 PHE A 747 TYR 0.018 0.002 TYR A1225 ARG 0.006 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PRO cc_start: 0.7137 (Cg_exo) cc_final: 0.6527 (Cg_endo) REVERT: A 83 LEU cc_start: 0.8865 (tt) cc_final: 0.8662 (tt) REVERT: A 93 PHE cc_start: 0.7739 (m-80) cc_final: 0.7238 (m-80) REVERT: A 192 TYR cc_start: 0.8081 (t80) cc_final: 0.7659 (t80) REVERT: A 272 MET cc_start: 0.8537 (mmp) cc_final: 0.8332 (mmm) REVERT: A 376 ASN cc_start: 0.8793 (t0) cc_final: 0.8496 (p0) REVERT: A 406 GLU cc_start: 0.8602 (mp0) cc_final: 0.8357 (mp0) REVERT: A 498 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7105 (mttt) REVERT: A 550 TYR cc_start: 0.8108 (p90) cc_final: 0.7790 (p90) REVERT: A 612 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 714 ARG cc_start: 0.6922 (pmt170) cc_final: 0.6604 (ptp90) REVERT: A 726 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (ttp-110) REVERT: A 825 TYR cc_start: 0.8789 (t80) cc_final: 0.8034 (t80) REVERT: A 1053 ASP cc_start: 0.7015 (t0) cc_final: 0.6808 (t0) REVERT: A 1089 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 1110 PHE cc_start: 0.8557 (t80) cc_final: 0.8330 (t80) REVERT: A 1137 ASN cc_start: 0.9151 (m110) cc_final: 0.8803 (m110) REVERT: A 1235 LEU cc_start: 0.8425 (tt) cc_final: 0.7987 (mt) outliers start: 57 outliers final: 23 residues processed: 286 average time/residue: 0.2354 time to fit residues: 92.3508 Evaluate side-chains 197 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 119 GLN A 136 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN A1024 ASN A1137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9753 Z= 0.263 Angle : 0.889 11.282 13296 Z= 0.427 Chirality : 0.053 0.284 1557 Planarity : 0.005 0.046 1664 Dihedral : 15.526 105.797 1844 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 3.74 % Allowed : 16.03 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1167 helix: 0.16 (0.21), residues: 611 sheet: -2.43 (0.52), residues: 89 loop : -2.03 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 27 HIS 0.006 0.001 HIS A1042 PHE 0.020 0.002 PHE A 504 TYR 0.031 0.002 TYR A 293 ARG 0.005 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.560 Fit side-chains REVERT: A 78 ARG cc_start: 0.8683 (tpt-90) cc_final: 0.8423 (tpp-160) REVERT: A 93 PHE cc_start: 0.7610 (m-80) cc_final: 0.7407 (m-80) REVERT: A 127 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.4530 (pm20) REVERT: A 192 TYR cc_start: 0.8088 (t80) cc_final: 0.7820 (t80) REVERT: A 220 MET cc_start: 0.6504 (ppp) cc_final: 0.6254 (ppp) REVERT: A 277 MET cc_start: 0.7721 (mmt) cc_final: 0.7278 (mmm) REVERT: A 288 PHE cc_start: 0.6351 (m-10) cc_final: 0.6060 (m-10) REVERT: A 376 ASN cc_start: 0.8233 (t0) cc_final: 0.8003 (p0) REVERT: A 714 ARG cc_start: 0.6899 (pmt170) cc_final: 0.6660 (ptp90) REVERT: A 740 PHE cc_start: 0.8159 (t80) cc_final: 0.7866 (t80) REVERT: A 751 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7138 (pt) REVERT: A 825 TYR cc_start: 0.8658 (t80) cc_final: 0.7926 (t80) REVERT: A 1005 ASP cc_start: 0.8910 (t0) cc_final: 0.8591 (t0) REVERT: A 1089 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 1097 ASP cc_start: 0.7667 (t70) cc_final: 0.7350 (t70) REVERT: A 1110 PHE cc_start: 0.8556 (t80) cc_final: 0.8314 (t80) REVERT: A 1127 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: A 1137 ASN cc_start: 0.9150 (m-40) cc_final: 0.8917 (m110) outliers start: 38 outliers final: 23 residues processed: 225 average time/residue: 0.1922 time to fit residues: 63.0532 Evaluate side-chains 185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9753 Z= 0.271 Angle : 0.820 10.927 13296 Z= 0.392 Chirality : 0.049 0.237 1557 Planarity : 0.005 0.038 1664 Dihedral : 13.567 105.193 1805 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 4.33 % Allowed : 18.58 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.90 (0.24), residues: 1167 helix: 0.49 (0.21), residues: 609 sheet: -1.95 (0.55), residues: 83 loop : -1.77 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 27 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.002 PHE A 504 TYR 0.013 0.002 TYR A 44 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5212 (tt0) cc_final: 0.4359 (tm-30) REVERT: A 78 ARG cc_start: 0.8688 (tpt-90) cc_final: 0.8415 (tpp-160) REVERT: A 93 PHE cc_start: 0.7568 (m-80) cc_final: 0.7276 (m-80) REVERT: A 127 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4601 (pm20) REVERT: A 277 MET cc_start: 0.7753 (mmt) cc_final: 0.7350 (mmm) REVERT: A 714 ARG cc_start: 0.7113 (pmt170) cc_final: 0.6747 (ptp-110) REVERT: A 751 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7246 (pt) REVERT: A 825 TYR cc_start: 0.8746 (t80) cc_final: 0.7978 (t80) REVERT: A 912 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6667 (mmt) REVERT: A 1089 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 1097 ASP cc_start: 0.7558 (t70) cc_final: 0.7345 (t70) REVERT: A 1110 PHE cc_start: 0.8506 (t80) cc_final: 0.8276 (t80) REVERT: A 1143 TRP cc_start: 0.8057 (t60) cc_final: 0.7829 (t60) outliers start: 44 outliers final: 29 residues processed: 199 average time/residue: 0.1812 time to fit residues: 53.7775 Evaluate side-chains 191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.0020 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9753 Z= 0.202 Angle : 0.772 10.404 13296 Z= 0.365 Chirality : 0.046 0.235 1557 Planarity : 0.004 0.040 1664 Dihedral : 11.888 108.503 1804 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 4.52 % Allowed : 20.75 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.63 (0.24), residues: 1167 helix: 0.73 (0.21), residues: 609 sheet: -1.85 (0.48), residues: 95 loop : -1.64 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 27 HIS 0.006 0.001 HIS A1042 PHE 0.023 0.001 PHE A 504 TYR 0.017 0.001 TYR A 192 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.008 Fit side-chains REVERT: A 43 GLU cc_start: 0.5193 (tt0) cc_final: 0.4502 (tm-30) REVERT: A 78 ARG cc_start: 0.8698 (tpt-90) cc_final: 0.8406 (tpp-160) REVERT: A 93 PHE cc_start: 0.7342 (m-80) cc_final: 0.6663 (m-80) REVERT: A 156 MET cc_start: 0.8423 (tmm) cc_final: 0.8213 (ppp) REVERT: A 277 MET cc_start: 0.7671 (mmt) cc_final: 0.7342 (mmm) REVERT: A 751 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7223 (pt) REVERT: A 825 TYR cc_start: 0.8686 (t80) cc_final: 0.8027 (t80) REVERT: A 912 MET cc_start: 0.6975 (mmp) cc_final: 0.6580 (mmt) REVERT: A 1089 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 1097 ASP cc_start: 0.7622 (t70) cc_final: 0.7318 (t0) REVERT: A 1106 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 1235 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8129 (mt) outliers start: 46 outliers final: 29 residues processed: 196 average time/residue: 0.1764 time to fit residues: 51.2626 Evaluate side-chains 187 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9753 Z= 0.197 Angle : 0.751 11.043 13296 Z= 0.360 Chirality : 0.046 0.234 1557 Planarity : 0.004 0.040 1664 Dihedral : 11.122 107.429 1799 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.08 % Favored : 93.74 % Rotamer: Outliers : 4.23 % Allowed : 21.83 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.52 (0.24), residues: 1167 helix: 0.82 (0.21), residues: 612 sheet: -2.00 (0.44), residues: 115 loop : -1.49 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 27 HIS 0.006 0.001 HIS A1042 PHE 0.027 0.001 PHE A 504 TYR 0.016 0.001 TYR A 44 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.124 Fit side-chains REVERT: A 43 GLU cc_start: 0.5288 (tt0) cc_final: 0.4611 (tm-30) REVERT: A 78 ARG cc_start: 0.8699 (tpt-90) cc_final: 0.8399 (tpp-160) REVERT: A 92 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7669 (pp30) REVERT: A 101 PHE cc_start: 0.8504 (t80) cc_final: 0.8032 (m-80) REVERT: A 277 MET cc_start: 0.7784 (mmt) cc_final: 0.7461 (mmm) REVERT: A 578 GLN cc_start: 0.8279 (mp10) cc_final: 0.8046 (mp-120) REVERT: A 825 TYR cc_start: 0.8784 (t80) cc_final: 0.8080 (t80) REVERT: A 912 MET cc_start: 0.6855 (mmp) cc_final: 0.6652 (mmt) REVERT: A 958 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7115 (mtm180) REVERT: A 991 GLN cc_start: 0.8634 (pp30) cc_final: 0.8425 (pp30) REVERT: A 1013 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6281 (mmmt) REVERT: A 1089 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 1097 ASP cc_start: 0.7569 (t70) cc_final: 0.7277 (t0) REVERT: A 1106 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 1202 ILE cc_start: 0.8275 (mp) cc_final: 0.7992 (mt) REVERT: A 1235 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8216 (mt) outliers start: 43 outliers final: 33 residues processed: 193 average time/residue: 0.1851 time to fit residues: 52.9575 Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9753 Z= 0.209 Angle : 0.748 11.506 13296 Z= 0.357 Chirality : 0.045 0.232 1557 Planarity : 0.004 0.042 1664 Dihedral : 10.701 103.580 1799 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 4.62 % Allowed : 22.91 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.38 (0.25), residues: 1167 helix: 0.92 (0.21), residues: 612 sheet: -1.89 (0.45), residues: 115 loop : -1.41 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 PHE 0.028 0.002 PHE A 504 TYR 0.021 0.001 TYR A 420 ARG 0.002 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5376 (tt0) cc_final: 0.4463 (tm-30) REVERT: A 78 ARG cc_start: 0.8685 (tpt-90) cc_final: 0.8375 (tpp-160) REVERT: A 101 PHE cc_start: 0.8501 (t80) cc_final: 0.8141 (m-80) REVERT: A 277 MET cc_start: 0.7786 (mmt) cc_final: 0.7446 (mmm) REVERT: A 506 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7457 (t80) REVERT: A 578 GLN cc_start: 0.8398 (mp10) cc_final: 0.8144 (mp10) REVERT: A 751 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7212 (pt) REVERT: A 825 TYR cc_start: 0.8781 (t80) cc_final: 0.8136 (t80) REVERT: A 912 MET cc_start: 0.6531 (mmp) cc_final: 0.6253 (mmt) REVERT: A 958 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7070 (mtm180) REVERT: A 1013 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6339 (mmmt) REVERT: A 1089 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 1097 ASP cc_start: 0.7530 (t70) cc_final: 0.7253 (t0) REVERT: A 1106 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 1235 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8223 (mt) outliers start: 47 outliers final: 33 residues processed: 194 average time/residue: 0.1914 time to fit residues: 55.5952 Evaluate side-chains 195 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9753 Z= 0.212 Angle : 0.761 12.916 13296 Z= 0.365 Chirality : 0.045 0.234 1557 Planarity : 0.004 0.042 1664 Dihedral : 10.224 96.004 1799 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.72 % Allowed : 22.32 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.25 (0.25), residues: 1167 helix: 0.99 (0.21), residues: 614 sheet: -1.47 (0.51), residues: 101 loop : -1.45 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 PHE 0.054 0.002 PHE A 93 TYR 0.016 0.001 TYR A 44 ARG 0.002 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7600 (m-80) cc_final: 0.7328 (m-80) REVERT: A 78 ARG cc_start: 0.8708 (tpt-90) cc_final: 0.8399 (tpp-160) REVERT: A 193 MET cc_start: 0.8685 (mmm) cc_final: 0.8034 (mpp) REVERT: A 277 MET cc_start: 0.7894 (mmt) cc_final: 0.7629 (mmm) REVERT: A 506 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7497 (t80) REVERT: A 578 GLN cc_start: 0.8357 (mp10) cc_final: 0.8105 (mp-120) REVERT: A 751 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7286 (pt) REVERT: A 825 TYR cc_start: 0.8795 (t80) cc_final: 0.8103 (t80) REVERT: A 912 MET cc_start: 0.6341 (mmp) cc_final: 0.6139 (mmt) REVERT: A 958 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7216 (mtm180) REVERT: A 1013 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6373 (mmmt) REVERT: A 1089 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 1097 ASP cc_start: 0.7508 (t70) cc_final: 0.7253 (t0) REVERT: A 1106 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 1235 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8224 (mt) outliers start: 48 outliers final: 34 residues processed: 193 average time/residue: 0.1821 time to fit residues: 52.2276 Evaluate side-chains 193 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9753 Z= 0.234 Angle : 0.771 11.430 13296 Z= 0.371 Chirality : 0.046 0.233 1557 Planarity : 0.004 0.043 1664 Dihedral : 9.835 84.180 1799 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.23 % Allowed : 23.21 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.22 (0.25), residues: 1167 helix: 0.95 (0.21), residues: 615 sheet: -1.30 (0.51), residues: 102 loop : -1.37 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 27 HIS 0.002 0.001 HIS A 758 PHE 0.031 0.002 PHE A 504 TYR 0.023 0.001 TYR A 420 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8667 (tpt-90) cc_final: 0.8364 (tpp-160) REVERT: A 101 PHE cc_start: 0.8511 (t80) cc_final: 0.7987 (m-80) REVERT: A 277 MET cc_start: 0.7823 (mmt) cc_final: 0.7553 (mmm) REVERT: A 293 TYR cc_start: 0.7470 (t80) cc_final: 0.7187 (t80) REVERT: A 506 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7562 (t80) REVERT: A 528 LEU cc_start: 0.7661 (mt) cc_final: 0.7306 (mm) REVERT: A 578 GLN cc_start: 0.8358 (mp10) cc_final: 0.8125 (mp-120) REVERT: A 770 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7687 (tt) REVERT: A 825 TYR cc_start: 0.8790 (t80) cc_final: 0.8119 (t80) REVERT: A 912 MET cc_start: 0.6252 (mmp) cc_final: 0.6002 (mmp) REVERT: A 958 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7225 (mtm180) REVERT: A 1013 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6581 (mmmt) REVERT: A 1089 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 1097 ASP cc_start: 0.7512 (t70) cc_final: 0.7263 (t0) REVERT: A 1106 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 1191 LEU cc_start: 0.8577 (tt) cc_final: 0.8354 (tt) REVERT: A 1235 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8245 (mt) outliers start: 43 outliers final: 34 residues processed: 184 average time/residue: 0.1966 time to fit residues: 53.7519 Evaluate side-chains 192 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 99 optimal weight: 0.0020 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.3046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9753 Z= 0.188 Angle : 0.753 11.912 13296 Z= 0.360 Chirality : 0.045 0.252 1557 Planarity : 0.004 0.040 1664 Dihedral : 9.083 81.176 1799 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.44 % Allowed : 23.99 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.09 (0.25), residues: 1167 helix: 1.09 (0.21), residues: 613 sheet: -1.12 (0.52), residues: 101 loop : -1.38 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1143 HIS 0.004 0.001 HIS A 758 PHE 0.032 0.002 PHE A 152 TYR 0.018 0.001 TYR A 44 ARG 0.002 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8676 (tpt-90) cc_final: 0.8344 (tpp-160) REVERT: A 101 PHE cc_start: 0.8454 (t80) cc_final: 0.7954 (m-80) REVERT: A 191 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7835 (mt-10) REVERT: A 277 MET cc_start: 0.7972 (mmt) cc_final: 0.7704 (mmm) REVERT: A 293 TYR cc_start: 0.7504 (t80) cc_final: 0.7198 (t80) REVERT: A 506 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 578 GLN cc_start: 0.8251 (mp10) cc_final: 0.8031 (mp10) REVERT: A 819 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6984 (tpt-90) REVERT: A 825 TYR cc_start: 0.8778 (t80) cc_final: 0.8167 (t80) REVERT: A 834 MET cc_start: 0.7419 (ttt) cc_final: 0.7150 (ttm) REVERT: A 912 MET cc_start: 0.5923 (mmp) cc_final: 0.5668 (mmp) REVERT: A 958 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7119 (mtm180) REVERT: A 1089 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 1097 ASP cc_start: 0.7476 (t70) cc_final: 0.7215 (t0) REVERT: A 1191 LEU cc_start: 0.8566 (tt) cc_final: 0.8342 (tt) REVERT: A 1235 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8224 (mt) outliers start: 35 outliers final: 27 residues processed: 188 average time/residue: 0.2015 time to fit residues: 57.4989 Evaluate side-chains 188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9753 Z= 0.201 Angle : 0.763 12.047 13296 Z= 0.368 Chirality : 0.045 0.248 1557 Planarity : 0.004 0.040 1664 Dihedral : 8.715 78.837 1792 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.05 % Allowed : 25.07 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.04 (0.25), residues: 1167 helix: 1.08 (0.21), residues: 614 sheet: -0.97 (0.51), residues: 102 loop : -1.31 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1143 HIS 0.003 0.001 HIS A 497 PHE 0.031 0.002 PHE A 152 TYR 0.025 0.001 TYR A 420 ARG 0.002 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7351 (p-90) cc_final: 0.6867 (t60) REVERT: A 101 PHE cc_start: 0.8430 (t80) cc_final: 0.7943 (m-80) REVERT: A 277 MET cc_start: 0.8014 (mmt) cc_final: 0.7746 (mmm) REVERT: A 506 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7593 (t80) REVERT: A 578 GLN cc_start: 0.8285 (mp10) cc_final: 0.8079 (mp10) REVERT: A 819 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6974 (tpt-90) REVERT: A 825 TYR cc_start: 0.8772 (t80) cc_final: 0.8283 (t80) REVERT: A 912 MET cc_start: 0.5696 (mmp) cc_final: 0.5478 (mmp) REVERT: A 958 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7132 (mtm180) REVERT: A 1050 ASP cc_start: 0.8125 (m-30) cc_final: 0.7813 (m-30) REVERT: A 1089 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 1097 ASP cc_start: 0.7500 (t70) cc_final: 0.7254 (t0) REVERT: A 1191 LEU cc_start: 0.8564 (tt) cc_final: 0.8342 (tt) REVERT: A 1235 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 31 outliers final: 27 residues processed: 175 average time/residue: 0.1809 time to fit residues: 47.8953 Evaluate side-chains 184 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112032 restraints weight = 16709.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114122 restraints weight = 9346.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114782 restraints weight = 7209.248| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9753 Z= 0.229 Angle : 0.777 13.246 13296 Z= 0.375 Chirality : 0.047 0.298 1557 Planarity : 0.004 0.041 1664 Dihedral : 8.573 76.556 1792 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 3.34 % Allowed : 25.17 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.05 (0.25), residues: 1167 helix: 1.09 (0.21), residues: 607 sheet: -0.95 (0.51), residues: 102 loop : -1.32 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1143 HIS 0.003 0.001 HIS A 497 PHE 0.031 0.002 PHE A 152 TYR 0.017 0.001 TYR A 709 ARG 0.004 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.92 seconds wall clock time: 37 minutes 39.79 seconds (2259.79 seconds total)