Starting phenix.real_space_refine on Sat Sep 12 10:25:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5u_21548/09_2026/6w5u_21548.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 70 5.16 5 C 6128 2.51 5 N 1495 2.21 5 O 1781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9474 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9158 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 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 chiralities: 2 Chain: "C" 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 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 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 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 chiralities: 9 Time building chain proxies: 1.71, per 1000 atoms: 0.18 Number of scatterers: 9474 At special positions: 0 Unit cell: (103.602, 91.348, 145.934, 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 70 16.00 O 1781 8.00 N 1495 7.00 C 6128 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=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 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=1.45 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=1.99 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 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=2.04 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 Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG C 2 " - " BMA 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: 0.83 Conformation dependent library (CDL) restraints added in 247.9 milliseconds 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: 52 helices and 5 sheets defined 60.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 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 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.793A pdb=" N LEU A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 195 removed outlier: 3.686A 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 294 removed outlier: 4.246A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 removed outlier: 4.281A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.141A 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 400 removed outlier: 3.605A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 436 through 453 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 542 through 545 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 594 removed outlier: 3.600A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.635A pdb=" N ASP A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 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 Processing helix chain 'A' and resid 824 through 830 removed outlier: 3.746A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.608A pdb=" N ILE A 837 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 removed outlier: 3.517A pdb=" N VAL A 856 " --> pdb=" O LEU A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 853 through 856' Processing helix chain 'A' and resid 870 through 883 removed outlier: 3.983A 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 942 through 951 Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.105A pdb=" N GLN A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 removed outlier: 4.224A 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 1015 through 1020 removed outlier: 3.989A pdb=" N SER A1020 " --> pdb=" O HIS A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.783A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 3.506A pdb=" N TYR A1085 " --> pdb=" O SER A1082 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1082 through 1086' Processing helix chain 'A' and resid 1089 through 1092 removed outlier: 3.691A pdb=" N LEU A1092 " --> pdb=" O GLU A1089 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1089 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 removed outlier: 3.580A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.907A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1177 removed outlier: 4.700A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1214 removed outlier: 4.397A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1242 removed outlier: 4.655A 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 27 through 35 removed outlier: 5.512A pdb=" N GLU A 30 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS A 42 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY A 32 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.820A pdb=" N LEU A 121 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A 146 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 123 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 144 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA A 125 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA5, first strand: chain 'A' and resid 1039 through 1043 494 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2877 1.34 - 1.46: 2333 1.46 - 1.58: 4407 1.58 - 1.71: 1 1.71 - 1.83: 99 Bond restraints: 9717 Sorted by residual: bond pdb=" C ALA A 165 " pdb=" N PRO A 166 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.25e-02 6.40e+03 1.17e+02 bond pdb=" C TYR A 56 " pdb=" N ASP A 57 " ideal model delta sigma weight residual 1.334 1.258 0.077 1.27e-02 6.20e+03 3.65e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.332 1.259 0.072 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C TYR A 102 " pdb=" N ASN A 103 " ideal model delta sigma weight residual 1.335 1.408 -0.074 1.36e-02 5.41e+03 2.93e+01 bond pdb=" C ASP A 170 " pdb=" N LYS A 171 " ideal model delta sigma weight residual 1.332 1.396 -0.064 1.40e-02 5.10e+03 2.09e+01 ... (remaining 9712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.42: 13200 8.42 - 16.83: 45 16.83 - 25.25: 0 25.25 - 33.66: 1 33.66 - 42.08: 1 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta sigma weight residual 110.49 152.57 -42.08 1.69e+00 3.50e-01 6.20e+02 angle pdb=" C ALA A 165 " pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta sigma weight residual 120.21 107.42 12.79 9.60e-01 1.09e+00 1.78e+02 angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" C LYS A 171 " ideal model delta sigma weight residual 110.80 84.63 26.17 2.13e+00 2.20e-01 1.51e+02 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 113.53 104.89 8.64 9.80e-01 1.04e+00 7.77e+01 angle pdb=" N GLN A 88 " pdb=" CA GLN A 88 " pdb=" C GLN A 88 " ideal model delta sigma weight residual 111.07 119.98 -8.91 1.07e+00 8.73e-01 6.94e+01 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4923 17.97 - 35.93: 481 35.93 - 53.90: 136 53.90 - 71.87: 31 71.87 - 89.83: 10 Dihedral angle restraints: 5581 sinusoidal: 2160 harmonic: 3421 Sorted by residual: dihedral pdb=" C ASP A 170 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual -122.60 -167.11 44.51 0 2.50e+00 1.60e-01 3.17e+02 dihedral pdb=" N ASP A 170 " pdb=" C ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual 122.80 165.01 -42.21 0 2.50e+00 1.60e-01 2.85e+02 dihedral pdb=" N LYS A 171 " pdb=" C LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta harmonic sigma weight residual 122.80 156.62 -33.82 0 2.50e+00 1.60e-01 1.83e+02 ... (remaining 5578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.950: 1552 0.950 - 1.899: 2 1.899 - 2.849: 1 2.849 - 3.798: 0 3.798 - 4.748: 1 Chirality restraints: 1556 Sorted by residual: 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 2.35 -4.75 2.00e-02 2.50e+03 5.63e+04 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.72e+02 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 -1.90 -0.50 2.00e-02 2.50e+03 6.14e+02 ... (remaining 1553 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.308 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C7 NAG D 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.301 2.00e-02 2.50e+03 2.53e-01 8.00e+02 pdb=" C7 NAG B 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " -0.128 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" CG ASN A 524 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " 0.259 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.342 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " 0.265 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 41 2.37 - 3.00: 6628 3.00 - 3.64: 14068 3.64 - 4.27: 21381 4.27 - 4.90: 35192 Nonbonded interactions: 77310 Sorted by model distance: nonbonded pdb=" OD1 ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.741 3.040 nonbonded pdb=" CG ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.856 2.616 nonbonded pdb=" O3 NAG A1402 " pdb=" O7 NAG A1402 " model vdw 1.982 3.040 nonbonded pdb=" OD2 ASP A 131 " pdb=" N THR A 134 " model vdw 2.035 3.120 nonbonded pdb=" N GLY A1181 " pdb=" OE2 GLU A1185 " model vdw 2.053 3.120 ... (remaining 77305 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' selection = chain 'D' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.014 0.580 9751 Z= 0.704 Angle : 1.871 52.142 13334 Z= 0.947 Chirality : 0.157 4.748 1556 Planarity : 0.012 0.260 1660 Dihedral : 15.822 89.833 3336 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 63.51 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.48 % Favored : 90.49 % Rotamer: Outliers : 6.82 % Allowed : 10.19 % Favored : 82.99 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.23), residues: 1167 helix: -0.93 (0.20), residues: 601 sheet: -2.10 (0.60), residues: 86 loop : -2.94 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 389 TYR 0.030 0.003 TYR A 423 PHE 0.040 0.004 PHE A 339 TRP 0.070 0.005 TRP A1145 HIS 0.010 0.003 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.56 ( 9717) covalent geometry : angle 1.52476 / 0.87 (13247) SS BOND : bond 0.15021 / 5.08 ( 15) SS BOND : angle 6.12718 / 3.64 ( 30) hydrogen bonds : bond 0.17073 / 10.92 ( 494) hydrogen bonds : angle 7.28854 / 4.99 ( 1431) link_BETA1-3 : bond 0.06645 / 3.50 ( 1) link_BETA1-3 : angle 27.62025 / 14.96 ( 3) link_BETA1-4 : bond 0.04069 / 2.49 ( 5) link_BETA1-4 : angle 12.28068 / 7.74 ( 15) link_NAG-ASN : bond 0.16788 / 7.16 ( 13) link_NAG-ASN : angle 16.18022 / 8.61 ( 39) *********************** 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 298 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8693 (m-40) cc_final: 0.8463 (m-40) REVERT: A 110 GLU cc_start: 0.8136 (tp30) cc_final: 0.7926 (tt0) REVERT: A 145 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6759 (mm110) REVERT: A 206 THR cc_start: 0.6262 (OUTLIER) cc_final: 0.6058 (p) REVERT: A 612 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: A 633 LEU cc_start: 0.9361 (tp) cc_final: 0.9134 (tt) REVERT: A 707 GLN cc_start: 0.8571 (mm110) cc_final: 0.8367 (mm110) REVERT: A 712 ASP cc_start: 0.8020 (t70) cc_final: 0.7672 (t0) REVERT: A 714 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7590 (pmt170) REVERT: A 754 MET cc_start: 0.7675 (tmm) cc_final: 0.7219 (ttp) REVERT: A 766 LEU cc_start: 0.8664 (tp) cc_final: 0.8397 (tp) REVERT: A 858 ILE cc_start: 0.9394 (mm) cc_final: 0.8589 (tt) REVERT: A 1114 MET cc_start: 0.8323 (tmm) cc_final: 0.7744 (tmm) REVERT: A 1143 TRP cc_start: 0.7858 (t60) cc_final: 0.7506 (t60) REVERT: A 1175 PHE cc_start: 0.8426 (t80) cc_final: 0.7919 (t80) REVERT: A 1222 GLN cc_start: 0.7866 (tt0) cc_final: 0.7388 (tm-30) outliers start: 69 outliers final: 23 residues processed: 276 average time/residue: 0.0865 time to fit residues: 34.0564 Evaluate side-chains 188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1116 LEU 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 122 ASN A 145 GLN A 150 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 349 ASN A 447 GLN A 489 GLN A 497 HIS A 530 HIS A 596 ASN A 775 GLN A 793 ASN A 884 HIS A1016 HIS A1137 ASN A1239 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101910 restraints weight = 17679.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102067 restraints weight = 10448.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102360 restraints weight = 10680.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103368 restraints weight = 7162.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105733 restraints weight = 6051.396| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9751 Z= 0.187 Angle : 0.955 13.034 13334 Z= 0.453 Chirality : 0.056 0.497 1556 Planarity : 0.005 0.045 1660 Dihedral : 9.248 99.001 1339 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.51 % Favored : 93.23 % Rotamer: Outliers : 4.85 % Allowed : 14.74 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1167 helix: 0.04 (0.20), residues: 616 sheet: -1.45 (0.55), residues: 88 loop : -1.99 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 978 TYR 0.034 0.002 TYR A 40 PHE 0.023 0.002 PHE A 998 TRP 0.054 0.002 TRP A 27 HIS 0.007 0.002 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 ( 9717) covalent geometry : angle 0.91262 / 0.44 (13247) SS BOND : bond 0.00646 / 0.40 ( 15) SS BOND : angle 2.49184 / 1.43 ( 30) hydrogen bonds : bond 0.05797 / 3.88 ( 494) hydrogen bonds : angle 5.59649 / 3.83 ( 1431) link_BETA1-3 : bond 0.01605 / 0.84 ( 1) link_BETA1-3 : angle 6.83188 / 3.63 ( 3) link_BETA1-4 : bond 0.01379 / 0.72 ( 5) link_BETA1-4 : angle 3.22002 / 1.99 ( 15) link_NAG-ASN : bond 0.00931 / 0.50 ( 13) link_NAG-ASN : angle 4.06242 / 2.85 ( 39) *********************** 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 253 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8319 (ttp-110) REVERT: A 107 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8846 (tp) REVERT: A 111 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 156 MET cc_start: 0.6500 (tmm) cc_final: 0.6178 (tmm) REVERT: A 222 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5660 (m110) REVERT: A 460 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: A 612 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8434 (tp30) REVERT: A 742 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6345 (mt-10) REVERT: A 766 LEU cc_start: 0.8763 (tp) cc_final: 0.8291 (tp) REVERT: A 858 ILE cc_start: 0.9226 (mm) cc_final: 0.8499 (tt) REVERT: A 872 MET cc_start: 0.8349 (mtp) cc_final: 0.8148 (mmt) REVERT: A 982 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8216 (tm) REVERT: A 991 GLN cc_start: 0.8540 (pt0) cc_final: 0.8312 (pt0) REVERT: A 1041 TYR cc_start: 0.9272 (m-80) cc_final: 0.8194 (m-80) REVERT: A 1106 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8973 (tt) REVERT: A 1114 MET cc_start: 0.8195 (tmm) cc_final: 0.7722 (tmm) REVERT: A 1143 TRP cc_start: 0.7994 (t60) cc_final: 0.7586 (t60) REVERT: A 1175 PHE cc_start: 0.8208 (t80) cc_final: 0.7902 (t80) REVERT: A 1179 MET cc_start: 0.6264 (mtm) cc_final: 0.5972 (ttp) outliers start: 49 outliers final: 23 residues processed: 239 average time/residue: 0.0851 time to fit residues: 29.4335 Evaluate side-chains 180 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.0000 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 884 HIS A1008 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101875 restraints weight = 17389.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101989 restraints weight = 10080.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102724 restraints weight = 9714.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103384 restraints weight = 6414.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103770 restraints weight = 5691.114| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9751 Z= 0.163 Angle : 0.835 11.688 13334 Z= 0.398 Chirality : 0.050 0.379 1556 Planarity : 0.005 0.050 1660 Dihedral : 7.826 104.355 1301 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.51 % Favored : 93.23 % Rotamer: Outliers : 3.96 % Allowed : 18.40 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1167 helix: 0.49 (0.21), residues: 613 sheet: -1.46 (0.50), residues: 95 loop : -1.60 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.023 0.002 TYR A 40 PHE 0.016 0.002 PHE A 488 TRP 0.046 0.002 TRP A 27 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9717) covalent geometry : angle 0.79878 / 0.39 (13247) SS BOND : bond 0.00456 / 0.25 ( 15) SS BOND : angle 1.82755 / 1.05 ( 30) hydrogen bonds : bond 0.05073 / 3.43 ( 494) hydrogen bonds : angle 5.27833 / 3.63 ( 1431) link_BETA1-3 : bond 0.01473 / 0.78 ( 1) link_BETA1-3 : angle 6.14733 / 3.28 ( 3) link_BETA1-4 : bond 0.00992 / 0.51 ( 5) link_BETA1-4 : angle 2.41638 / 1.48 ( 15) link_NAG-ASN : bond 0.00613 / 0.36 ( 13) link_NAG-ASN : angle 3.71076 / 2.59 ( 39) *********************** 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 218 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8394 (ttp-110) REVERT: A 103 ASN cc_start: 0.8776 (m-40) cc_final: 0.8456 (m-40) REVERT: A 217 MET cc_start: 0.2363 (mmt) cc_final: 0.2106 (mmt) REVERT: A 222 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5879 (m110) REVERT: A 488 PHE cc_start: 0.8955 (m-80) cc_final: 0.8671 (m-10) REVERT: A 653 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8116 (mppt) REVERT: A 697 VAL cc_start: 0.7745 (m) cc_final: 0.7537 (t) REVERT: A 742 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6172 (mt-10) REVERT: A 766 LEU cc_start: 0.8763 (tp) cc_final: 0.8298 (tp) REVERT: A 858 ILE cc_start: 0.9276 (mm) cc_final: 0.8603 (tt) REVERT: A 872 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8191 (mmt) REVERT: A 909 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8386 (p) REVERT: A 991 GLN cc_start: 0.8580 (pt0) cc_final: 0.8300 (pt0) REVERT: A 1106 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 1114 MET cc_start: 0.8145 (tmm) cc_final: 0.7590 (tmm) REVERT: A 1143 TRP cc_start: 0.7923 (t60) cc_final: 0.7565 (t60) REVERT: A 1175 PHE cc_start: 0.8129 (t80) cc_final: 0.7868 (t80) REVERT: A 1179 MET cc_start: 0.6196 (mtm) cc_final: 0.5886 (ttp) outliers start: 40 outliers final: 26 residues processed: 203 average time/residue: 0.0753 time to fit residues: 22.4676 Evaluate side-chains 187 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099130 restraints weight = 17942.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099992 restraints weight = 10119.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101384 restraints weight = 7948.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101643 restraints weight = 6054.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102022 restraints weight = 5682.466| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9751 Z= 0.182 Angle : 0.822 10.901 13334 Z= 0.391 Chirality : 0.050 0.317 1556 Planarity : 0.005 0.039 1660 Dihedral : 7.042 59.797 1295 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 5.04 % Allowed : 18.99 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1167 helix: 0.56 (0.21), residues: 619 sheet: -1.41 (0.50), residues: 95 loop : -1.56 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 978 TYR 0.031 0.002 TYR A 515 PHE 0.031 0.002 PHE A 504 TRP 0.041 0.002 TRP A 27 HIS 0.009 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9717) covalent geometry : angle 0.79071 / 0.38 (13247) SS BOND : bond 0.00552 / 0.36 ( 15) SS BOND : angle 1.91488 / 1.11 ( 30) hydrogen bonds : bond 0.04994 / 3.40 ( 494) hydrogen bonds : angle 5.16874 / 3.56 ( 1431) link_BETA1-3 : bond 0.01370 / 0.72 ( 1) link_BETA1-3 : angle 5.44504 / 2.92 ( 3) link_BETA1-4 : bond 0.00929 / 0.48 ( 5) link_BETA1-4 : angle 2.16338 / 1.33 ( 15) link_NAG-ASN : bond 0.00554 / 0.30 ( 13) link_NAG-ASN : angle 3.43078 / 2.38 ( 39) *********************** 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 210 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8617 (mtm110) cc_final: 0.8379 (ttp-110) REVERT: A 103 ASN cc_start: 0.8694 (m-40) cc_final: 0.8365 (m-40) REVERT: A 156 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5999 (tmm) REVERT: A 222 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6114 (m110) REVERT: A 460 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: A 488 PHE cc_start: 0.8967 (m-80) cc_final: 0.8660 (m-10) REVERT: A 742 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6191 (mt-10) REVERT: A 766 LEU cc_start: 0.8828 (tp) cc_final: 0.8387 (tp) REVERT: A 858 ILE cc_start: 0.9382 (mm) cc_final: 0.8702 (tt) REVERT: A 889 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8870 (t) REVERT: A 909 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 991 GLN cc_start: 0.8589 (pt0) cc_final: 0.8307 (pt0) REVERT: A 1026 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7712 (pp) REVERT: A 1114 MET cc_start: 0.8078 (tmm) cc_final: 0.7566 (tmm) REVERT: A 1143 TRP cc_start: 0.7967 (t60) cc_final: 0.7683 (t60) REVERT: A 1175 PHE cc_start: 0.8174 (t80) cc_final: 0.7872 (t80) REVERT: A 1179 MET cc_start: 0.5920 (mtm) cc_final: 0.5669 (ttp) REVERT: A 1193 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7134 (t-90) outliers start: 51 outliers final: 33 residues processed: 199 average time/residue: 0.0834 time to fit residues: 24.2165 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 75 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103001 restraints weight = 17672.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102440 restraints weight = 10877.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103678 restraints weight = 9235.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104193 restraints weight = 6553.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104424 restraints weight = 6399.487| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9751 Z= 0.182 Angle : 0.854 21.334 13334 Z= 0.398 Chirality : 0.057 1.096 1556 Planarity : 0.005 0.035 1660 Dihedral : 7.058 64.084 1294 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 5.04 % Allowed : 19.78 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.25), residues: 1167 helix: 0.64 (0.21), residues: 618 sheet: -1.34 (0.51), residues: 95 loop : -1.54 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 389 TYR 0.029 0.002 TYR A 457 PHE 0.035 0.002 PHE A 504 TRP 0.024 0.002 TRP A 27 HIS 0.008 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9717) covalent geometry : angle 0.79406 / 0.38 (13247) SS BOND : bond 0.00416 / 0.25 ( 15) SS BOND : angle 1.73348 / 1.00 ( 30) hydrogen bonds : bond 0.04933 / 3.34 ( 494) hydrogen bonds : angle 5.12598 / 3.53 ( 1431) link_BETA1-3 : bond 0.01107 / 0.58 ( 1) link_BETA1-3 : angle 5.27034 / 2.83 ( 3) link_BETA1-4 : bond 0.00945 / 0.49 ( 5) link_BETA1-4 : angle 2.10029 / 1.30 ( 15) link_NAG-ASN : bond 0.00682 / 0.38 ( 13) link_NAG-ASN : angle 5.38337 / 3.15 ( 39) *********************** 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 206 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8600 (m-40) cc_final: 0.8337 (m-40) REVERT: A 156 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6021 (tmm) REVERT: A 217 MET cc_start: 0.2069 (mmt) cc_final: 0.1750 (mmt) REVERT: A 220 MET cc_start: 0.7837 (tmm) cc_final: 0.7496 (tmm) REVERT: A 222 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.5969 (m110) REVERT: A 488 PHE cc_start: 0.8915 (m-80) cc_final: 0.8624 (m-10) REVERT: A 742 GLU cc_start: 0.6419 (mt-10) cc_final: 0.6118 (mt-10) REVERT: A 766 LEU cc_start: 0.8964 (tp) cc_final: 0.8564 (tp) REVERT: A 858 ILE cc_start: 0.9367 (mm) cc_final: 0.8760 (tt) REVERT: A 889 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8896 (t) REVERT: A 909 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8509 (p) REVERT: A 991 GLN cc_start: 0.8595 (pt0) cc_final: 0.8337 (pt0) REVERT: A 1026 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7681 (pp) REVERT: A 1114 MET cc_start: 0.8021 (tmm) cc_final: 0.7532 (tmm) REVERT: A 1143 TRP cc_start: 0.7906 (t60) cc_final: 0.7644 (t60) REVERT: A 1175 PHE cc_start: 0.8190 (t80) cc_final: 0.7886 (t80) REVERT: A 1193 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7183 (t-90) outliers start: 51 outliers final: 36 residues processed: 196 average time/residue: 0.0870 time to fit residues: 24.6469 Evaluate side-chains 187 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 0.0040 chunk 28 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105252 restraints weight = 17426.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105568 restraints weight = 9999.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106353 restraints weight = 8762.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106971 restraints weight = 6483.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107928 restraints weight = 6199.319| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9751 Z= 0.143 Angle : 0.805 18.534 13334 Z= 0.376 Chirality : 0.048 0.283 1556 Planarity : 0.004 0.044 1660 Dihedral : 6.504 58.417 1291 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 5.34 % Allowed : 19.98 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.25), residues: 1167 helix: 0.73 (0.21), residues: 610 sheet: -0.98 (0.55), residues: 94 loop : -1.41 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 978 TYR 0.020 0.001 TYR A 515 PHE 0.022 0.001 PHE A 504 TRP 0.025 0.001 TRP A 27 HIS 0.009 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9717) covalent geometry : angle 0.76093 / 0.37 (13247) SS BOND : bond 0.00602 / 0.45 ( 15) SS BOND : angle 1.63868 / 0.93 ( 30) hydrogen bonds : bond 0.04601 / 3.17 ( 494) hydrogen bonds : angle 5.00619 / 3.45 ( 1431) link_BETA1-3 : bond 0.01219 / 0.64 ( 1) link_BETA1-3 : angle 4.80787 / 2.57 ( 3) link_BETA1-4 : bond 0.00929 / 0.48 ( 5) link_BETA1-4 : angle 1.94002 / 1.20 ( 15) link_NAG-ASN : bond 0.00967 / 0.49 ( 13) link_NAG-ASN : angle 4.43091 / 2.71 ( 39) *********************** 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 217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8236 (ttp-110) REVERT: A 92 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8013 (mm-40) REVERT: A 103 ASN cc_start: 0.8722 (m-40) cc_final: 0.8443 (m-40) REVERT: A 146 TYR cc_start: 0.6561 (t80) cc_final: 0.6350 (t80) REVERT: A 156 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.5936 (tmm) REVERT: A 460 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: A 766 LEU cc_start: 0.8891 (tp) cc_final: 0.8565 (tp) REVERT: A 858 ILE cc_start: 0.9342 (mm) cc_final: 0.8681 (tt) REVERT: A 909 CYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 944 ASP cc_start: 0.8079 (p0) cc_final: 0.7863 (p0) REVERT: A 991 GLN cc_start: 0.8534 (pt0) cc_final: 0.8302 (pt0) REVERT: A 1008 ASN cc_start: 0.7913 (m110) cc_final: 0.7638 (m110) REVERT: A 1026 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 1114 MET cc_start: 0.7965 (tmm) cc_final: 0.7495 (tmm) REVERT: A 1143 TRP cc_start: 0.7904 (t60) cc_final: 0.7522 (t60) REVERT: A 1175 PHE cc_start: 0.8132 (t80) cc_final: 0.7830 (t80) REVERT: A 1179 MET cc_start: 0.5736 (mtm) cc_final: 0.5416 (ttp) REVERT: A 1193 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7102 (t-90) outliers start: 54 outliers final: 36 residues processed: 204 average time/residue: 0.0779 time to fit residues: 23.5245 Evaluate side-chains 192 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1008 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103744 restraints weight = 17596.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103598 restraints weight = 10405.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104460 restraints weight = 8993.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104991 restraints weight = 6717.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105258 restraints weight = 6458.070| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9751 Z= 0.168 Angle : 0.827 19.475 13334 Z= 0.389 Chirality : 0.048 0.291 1556 Planarity : 0.004 0.036 1660 Dihedral : 6.582 59.573 1291 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.95 % Allowed : 21.86 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1167 helix: 0.70 (0.21), residues: 617 sheet: -1.18 (0.54), residues: 94 loop : -1.38 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 978 TYR 0.018 0.001 TYR A 40 PHE 0.024 0.002 PHE A1167 TRP 0.024 0.002 TRP A 27 HIS 0.007 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 9717) covalent geometry : angle 0.77801 / 0.38 (13247) SS BOND : bond 0.00472 / 0.32 ( 15) SS BOND : angle 2.35612 / 1.33 ( 30) hydrogen bonds : bond 0.04745 / 3.26 ( 494) hydrogen bonds : angle 5.01317 / 3.45 ( 1431) link_BETA1-3 : bond 0.01088 / 0.57 ( 1) link_BETA1-3 : angle 4.60305 / 2.46 ( 3) link_BETA1-4 : bond 0.00941 / 0.49 ( 5) link_BETA1-4 : angle 1.95935 / 1.23 ( 15) link_NAG-ASN : bond 0.00907 / 0.47 ( 13) link_NAG-ASN : angle 4.54876 / 2.74 ( 39) *********************** 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: 50 poor density : 161 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8150 (ttp-110) REVERT: A 103 ASN cc_start: 0.8722 (m-40) cc_final: 0.8450 (m-40) REVERT: A 146 TYR cc_start: 0.6556 (t80) cc_final: 0.6351 (t80) REVERT: A 156 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.5984 (tmm) REVERT: A 220 MET cc_start: 0.7513 (tmm) cc_final: 0.6809 (tmm) REVERT: A 222 ASN cc_start: 0.6525 (OUTLIER) cc_final: 0.5803 (m110) REVERT: A 766 LEU cc_start: 0.8931 (tp) cc_final: 0.8540 (tp) REVERT: A 858 ILE cc_start: 0.9369 (mm) cc_final: 0.8692 (tt) REVERT: A 864 LEU cc_start: 0.7503 (pt) cc_final: 0.6847 (mt) REVERT: A 909 CYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 991 GLN cc_start: 0.8540 (pt0) cc_final: 0.8332 (pt0) REVERT: A 1008 ASN cc_start: 0.8099 (m-40) cc_final: 0.7873 (m110) REVERT: A 1026 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7771 (pp) REVERT: A 1114 MET cc_start: 0.7845 (tmm) cc_final: 0.7289 (tmm) REVERT: A 1143 TRP cc_start: 0.7962 (t60) cc_final: 0.7722 (t60) REVERT: A 1175 PHE cc_start: 0.8138 (t80) cc_final: 0.7828 (t80) outliers start: 50 outliers final: 43 residues processed: 199 average time/residue: 0.0845 time to fit residues: 24.7705 Evaluate side-chains 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104736 restraints weight = 17601.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104698 restraints weight = 10454.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105343 restraints weight = 8751.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106237 restraints weight = 6788.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106408 restraints weight = 6310.425| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9751 Z= 0.150 Angle : 0.809 19.726 13334 Z= 0.381 Chirality : 0.047 0.282 1556 Planarity : 0.004 0.037 1660 Dihedral : 6.525 59.848 1291 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 4.75 % Allowed : 22.35 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1167 helix: 0.76 (0.21), residues: 617 sheet: -1.26 (0.54), residues: 94 loop : -1.35 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.018 0.001 TYR A 40 PHE 0.030 0.001 PHE A1110 TRP 0.024 0.002 TRP A 27 HIS 0.014 0.002 HIS A1193 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9717) covalent geometry : angle 0.76268 / 0.37 (13247) SS BOND : bond 0.00422 / 0.28 ( 15) SS BOND : angle 2.19816 / 1.25 ( 30) hydrogen bonds : bond 0.04609 / 3.17 ( 494) hydrogen bonds : angle 4.98994 / 3.43 ( 1431) link_BETA1-3 : bond 0.01078 / 0.57 ( 1) link_BETA1-3 : angle 4.40467 / 2.35 ( 3) link_BETA1-4 : bond 0.00948 / 0.48 ( 5) link_BETA1-4 : angle 1.89799 / 1.19 ( 15) link_NAG-ASN : bond 0.00865 / 0.45 ( 13) link_NAG-ASN : angle 4.45575 / 2.66 ( 39) *********************** 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 204 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8091 (ttp-110) REVERT: A 103 ASN cc_start: 0.8733 (m-40) cc_final: 0.8460 (m-40) REVERT: A 156 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5820 (tmm) REVERT: A 220 MET cc_start: 0.7300 (tmm) cc_final: 0.6657 (tmm) REVERT: A 222 ASN cc_start: 0.6476 (OUTLIER) cc_final: 0.5614 (m110) REVERT: A 662 LEU cc_start: 0.8122 (mp) cc_final: 0.7849 (mp) REVERT: A 766 LEU cc_start: 0.8928 (tp) cc_final: 0.8621 (tp) REVERT: A 858 ILE cc_start: 0.9358 (mm) cc_final: 0.8658 (tt) REVERT: A 864 LEU cc_start: 0.7450 (pt) cc_final: 0.6853 (mt) REVERT: A 944 ASP cc_start: 0.8130 (p0) cc_final: 0.7917 (p0) REVERT: A 991 GLN cc_start: 0.8493 (pt0) cc_final: 0.8283 (pt0) REVERT: A 1026 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7838 (pp) REVERT: A 1114 MET cc_start: 0.7887 (tmm) cc_final: 0.7359 (tmm) REVERT: A 1143 TRP cc_start: 0.7957 (t60) cc_final: 0.7695 (t60) REVERT: A 1175 PHE cc_start: 0.8093 (t80) cc_final: 0.7778 (t80) REVERT: A 1193 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7193 (t-90) outliers start: 48 outliers final: 41 residues processed: 191 average time/residue: 0.0877 time to fit residues: 24.6659 Evaluate side-chains 195 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN A1008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102195 restraints weight = 17800.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101714 restraints weight = 10531.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102528 restraints weight = 9672.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103152 restraints weight = 7018.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103313 restraints weight = 6509.119| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9751 Z= 0.192 Angle : 0.834 19.534 13334 Z= 0.398 Chirality : 0.048 0.312 1556 Planarity : 0.005 0.048 1660 Dihedral : 6.600 59.030 1291 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.85 % Allowed : 22.85 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1167 helix: 0.79 (0.21), residues: 609 sheet: -1.60 (0.50), residues: 95 loop : -1.39 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 978 TYR 0.022 0.002 TYR A 628 PHE 0.025 0.002 PHE A1110 TRP 0.022 0.002 TRP A 27 HIS 0.007 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 9717) covalent geometry : angle 0.78950 / 0.39 (13247) SS BOND : bond 0.00433 / 0.30 ( 15) SS BOND : angle 2.23958 / 1.30 ( 30) hydrogen bonds : bond 0.05009 / 3.44 ( 494) hydrogen bonds : angle 5.05730 / 3.45 ( 1431) link_BETA1-3 : bond 0.01072 / 0.56 ( 1) link_BETA1-3 : angle 4.03324 / 2.15 ( 3) link_BETA1-4 : bond 0.00961 / 0.49 ( 5) link_BETA1-4 : angle 1.92636 / 1.22 ( 15) link_NAG-ASN : bond 0.00851 / 0.42 ( 13) link_NAG-ASN : angle 4.43554 / 2.66 ( 39) *********************** 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 209 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8517 (mtm110) cc_final: 0.8217 (ttp-110) REVERT: A 103 ASN cc_start: 0.8728 (m-40) cc_final: 0.8467 (m-40) REVERT: A 156 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5903 (tmm) REVERT: A 222 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.5900 (m110) REVERT: A 662 LEU cc_start: 0.8225 (mp) cc_final: 0.7946 (mp) REVERT: A 766 LEU cc_start: 0.8987 (tp) cc_final: 0.8607 (tp) REVERT: A 864 LEU cc_start: 0.7383 (pt) cc_final: 0.6642 (mt) REVERT: A 909 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (p) REVERT: A 1026 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7779 (pp) REVERT: A 1090 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: A 1114 MET cc_start: 0.7839 (tmm) cc_final: 0.7284 (tmm) REVERT: A 1143 TRP cc_start: 0.7996 (t60) cc_final: 0.7744 (t60) REVERT: A 1175 PHE cc_start: 0.8160 (t80) cc_final: 0.7819 (t80) outliers start: 49 outliers final: 41 residues processed: 196 average time/residue: 0.0894 time to fit residues: 25.8834 Evaluate side-chains 195 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A1008 ASN A1193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101642 restraints weight = 17874.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100663 restraints weight = 11129.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102118 restraints weight = 9353.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102546 restraints weight = 6769.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102624 restraints weight = 6646.041| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9751 Z= 0.225 Angle : 0.870 19.457 13334 Z= 0.418 Chirality : 0.050 0.318 1556 Planarity : 0.005 0.036 1660 Dihedral : 6.633 58.156 1291 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 5.04 % Allowed : 23.24 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1167 helix: 0.73 (0.21), residues: 604 sheet: -1.80 (0.49), residues: 93 loop : -1.55 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 978 TYR 0.019 0.002 TYR A 628 PHE 0.024 0.002 PHE A1110 TRP 0.020 0.002 TRP A 27 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 9717) covalent geometry : angle 0.82734 / 0.41 (13247) SS BOND : bond 0.00521 / 0.37 ( 15) SS BOND : angle 2.25024 / 1.31 ( 30) hydrogen bonds : bond 0.05181 / 3.54 ( 494) hydrogen bonds : angle 5.18092 / 3.54 ( 1431) link_BETA1-3 : bond 0.00756 / 0.40 ( 1) link_BETA1-3 : angle 4.17486 / 2.22 ( 3) link_BETA1-4 : bond 0.00926 / 0.47 ( 5) link_BETA1-4 : angle 1.87121 / 1.21 ( 15) link_NAG-ASN : bond 0.00856 / 0.42 ( 13) link_NAG-ASN : angle 4.47096 / 2.69 ( 39) ********************** 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 202 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8256 (ttp-110) REVERT: A 103 ASN cc_start: 0.8651 (m-40) cc_final: 0.8407 (m-40) REVERT: A 156 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5736 (tmm) REVERT: A 222 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6181 (m110) REVERT: A 766 LEU cc_start: 0.9020 (tp) cc_final: 0.8632 (tp) REVERT: A 864 LEU cc_start: 0.7477 (pt) cc_final: 0.6748 (mt) REVERT: A 909 CYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 1026 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7904 (pp) REVERT: A 1090 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: A 1114 MET cc_start: 0.7913 (tmm) cc_final: 0.7340 (tmm) REVERT: A 1143 TRP cc_start: 0.7943 (t60) cc_final: 0.7697 (t60) REVERT: A 1175 PHE cc_start: 0.8181 (t80) cc_final: 0.7830 (t80) outliers start: 51 outliers final: 45 residues processed: 189 average time/residue: 0.0880 time to fit residues: 24.5323 Evaluate side-chains 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 ASN A1193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103021 restraints weight = 17696.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102441 restraints weight = 10965.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103624 restraints weight = 9379.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104159 restraints weight = 6695.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104274 restraints weight = 6510.130| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9751 Z= 0.175 Angle : 0.844 19.602 13334 Z= 0.402 Chirality : 0.049 0.304 1556 Planarity : 0.004 0.036 1660 Dihedral : 6.596 57.551 1291 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 4.85 % Allowed : 23.44 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1167 helix: 0.70 (0.21), residues: 615 sheet: -1.61 (0.51), residues: 95 loop : -1.52 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.028 0.002 TYR A 515 PHE 0.034 0.002 PHE A1167 TRP 0.019 0.002 TRP A 27 HIS 0.012 0.001 HIS A1193 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9717) covalent geometry : angle 0.80068 / 0.39 (13247) SS BOND : bond 0.00468 / 0.33 ( 15) SS BOND : angle 2.17641 / 1.24 ( 30) hydrogen bonds : bond 0.05023 / 3.43 ( 494) hydrogen bonds : angle 5.14236 / 3.53 ( 1431) link_BETA1-3 : bond 0.01175 / 0.62 ( 1) link_BETA1-3 : angle 4.00659 / 2.13 ( 3) link_BETA1-4 : bond 0.00914 / 0.47 ( 5) link_BETA1-4 : angle 1.80022 / 1.15 ( 15) link_NAG-ASN : bond 0.00875 / 0.44 ( 13) link_NAG-ASN : angle 4.41535 / 2.64 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.46 seconds wall clock time: 27 minutes 25.08 seconds (1645.08 seconds total)