Starting phenix.real_space_refine on Wed Mar 4 17:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5u_21548/03_2026/6w5u_21548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5u_21548/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6w5u_21548/03_2026/6w5u_21548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5u_21548/03_2026/6w5u_21548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w5u_21548/03_2026/6w5u_21548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5u_21548/03_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-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 2.23, per 1000 atoms: 0.24 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: 0.94 Conformation dependent library (CDL) restraints added in 468.9 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: 0.32 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: 1.54 Time building geometry restraints manager: 1.21 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 - 24.60: 5550 24.60 - 49.20: 376 49.20 - 73.79: 103 73.79 - 98.39: 24 98.39 - 122.99: 35 Dihedral angle restraints: 6088 sinusoidal: 2667 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 6085 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 20.438 122.991 3843 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 covalent geometry : bond 0.01127 ( 9717) covalent geometry : angle 1.52476 (13247) SS BOND : bond 0.15021 ( 15) SS BOND : angle 6.12718 ( 30) hydrogen bonds : bond 0.17073 ( 494) hydrogen bonds : angle 7.28854 ( 1431) link_BETA1-3 : bond 0.06645 ( 1) link_BETA1-3 : angle 27.62025 ( 3) link_BETA1-4 : bond 0.04069 ( 5) link_BETA1-4 : angle 12.28068 ( 15) link_NAG-ASN : bond 0.16788 ( 13) link_NAG-ASN : angle 16.18022 ( 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 : 0.383 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: 0.0871 time to fit residues: 34.1338 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 : 0.335 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 122 ASN A 145 GLN A 150 GLN A 215 HIS A 349 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102246 restraints weight = 17682.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102343 restraints weight = 10438.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102642 restraints weight = 10800.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103653 restraints weight = 7160.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105057 restraints weight = 6037.751| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9751 Z= 0.189 Angle : 1.000 12.933 13334 Z= 0.465 Chirality : 0.057 0.470 1556 Planarity : 0.005 0.045 1660 Dihedral : 17.950 116.712 1846 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.26 % Favored : 93.49 % Rotamer: Outliers : 4.75 % Allowed : 14.84 % 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: -1.31 (0.24), residues: 1167 helix: 0.06 (0.20), residues: 616 sheet: -1.47 (0.55), residues: 88 loop : -1.98 (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 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9717) covalent geometry : angle 0.94898 (13247) SS BOND : bond 0.00637 ( 15) SS BOND : angle 2.48468 ( 30) hydrogen bonds : bond 0.05694 ( 494) hydrogen bonds : angle 5.58050 ( 1431) link_BETA1-3 : bond 0.01474 ( 1) link_BETA1-3 : angle 7.18298 ( 3) link_BETA1-4 : bond 0.01412 ( 5) link_BETA1-4 : angle 4.67198 ( 15) link_NAG-ASN : bond 0.00962 ( 13) link_NAG-ASN : angle 4.34316 ( 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 254 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8578 (mtm110) cc_final: 0.8344 (ttp-110) REVERT: A 107 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 111 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 222 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5639 (m110) REVERT: A 460 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: A 612 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: A 712 ASP cc_start: 0.7993 (t70) cc_final: 0.7784 (t0) REVERT: A 742 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6299 (mt-10) REVERT: A 754 MET cc_start: 0.7281 (tmm) cc_final: 0.6755 (ttt) REVERT: A 766 LEU cc_start: 0.8777 (tp) cc_final: 0.8310 (tp) REVERT: A 858 ILE cc_start: 0.9238 (mm) cc_final: 0.8419 (tt) REVERT: A 872 MET cc_start: 0.8342 (mtp) cc_final: 0.8141 (mmt) REVERT: A 982 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8330 (tm) REVERT: A 991 GLN cc_start: 0.8550 (pt0) cc_final: 0.8323 (pt0) REVERT: A 1041 TYR cc_start: 0.9326 (m-80) cc_final: 0.8272 (m-80) REVERT: A 1106 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8953 (tt) REVERT: A 1114 MET cc_start: 0.8156 (tmm) cc_final: 0.7669 (tmm) REVERT: A 1143 TRP cc_start: 0.8008 (t60) cc_final: 0.7608 (t60) REVERT: A 1175 PHE cc_start: 0.8191 (t80) cc_final: 0.7876 (t80) REVERT: A 1179 MET cc_start: 0.6268 (mtm) cc_final: 0.5989 (ttp) outliers start: 48 outliers final: 23 residues processed: 240 average time/residue: 0.0824 time to fit residues: 28.4615 Evaluate side-chains 181 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 884 HIS A1008 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097723 restraints weight = 17802.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096454 restraints weight = 10755.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097321 restraints weight = 11228.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098045 restraints weight = 7381.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099707 restraints weight = 6438.889| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9751 Z= 0.254 Angle : 0.918 11.636 13334 Z= 0.440 Chirality : 0.054 0.343 1556 Planarity : 0.005 0.052 1660 Dihedral : 16.142 105.588 1808 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 4.85 % Allowed : 19.19 % Favored : 75.96 % 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: -1.06 (0.24), residues: 1167 helix: 0.28 (0.20), residues: 617 sheet: -1.64 (0.51), residues: 93 loop : -1.81 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.021 0.002 TYR A 40 PHE 0.018 0.002 PHE A 924 TRP 0.046 0.003 TRP A 27 HIS 0.010 0.002 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9717) covalent geometry : angle 0.87862 (13247) SS BOND : bond 0.00487 ( 15) SS BOND : angle 1.86100 ( 30) hydrogen bonds : bond 0.05721 ( 494) hydrogen bonds : angle 5.42327 ( 1431) link_BETA1-3 : bond 0.01011 ( 1) link_BETA1-3 : angle 6.74439 ( 3) link_BETA1-4 : bond 0.00592 ( 5) link_BETA1-4 : angle 3.01391 ( 15) link_NAG-ASN : bond 0.00443 ( 13) link_NAG-ASN : angle 4.02209 ( 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 207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8356 (ttp-110) REVERT: A 103 ASN cc_start: 0.8773 (m-40) cc_final: 0.8477 (m-40) REVERT: A 146 TYR cc_start: 0.6569 (t80) cc_final: 0.6362 (t80) REVERT: A 217 MET cc_start: 0.2405 (mmt) cc_final: 0.2103 (mmt) REVERT: A 222 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.5866 (m110) REVERT: A 452 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: A 488 PHE cc_start: 0.9026 (m-80) cc_final: 0.8738 (m-10) REVERT: A 742 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6264 (mt-10) REVERT: A 766 LEU cc_start: 0.8903 (tp) cc_final: 0.8692 (tp) REVERT: A 858 ILE cc_start: 0.9430 (mm) cc_final: 0.8743 (tt) REVERT: A 909 CYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 991 GLN cc_start: 0.8714 (pt0) cc_final: 0.8425 (pt0) REVERT: A 1106 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9044 (tt) REVERT: A 1114 MET cc_start: 0.8244 (tmm) cc_final: 0.7695 (tmm) REVERT: A 1143 TRP cc_start: 0.7997 (t60) cc_final: 0.7631 (t60) REVERT: A 1175 PHE cc_start: 0.8250 (t80) cc_final: 0.7899 (t80) outliers start: 49 outliers final: 35 residues processed: 193 average time/residue: 0.0789 time to fit residues: 22.3006 Evaluate side-chains 184 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 102 TYR 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 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 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 452 ASN 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 699 VAL 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 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 1048 SER Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1161 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 154 ASN A1006 ASN A1008 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.129803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101167 restraints weight = 17819.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099564 restraints weight = 10871.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100631 restraints weight = 10176.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101233 restraints weight = 7079.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101574 restraints weight = 6406.237| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9751 Z= 0.150 Angle : 0.826 11.088 13334 Z= 0.387 Chirality : 0.049 0.318 1556 Planarity : 0.004 0.037 1660 Dihedral : 14.346 102.550 1802 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 5.34 % Allowed : 18.89 % Favored : 75.77 % 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: -0.67 (0.25), residues: 1167 helix: 0.58 (0.21), residues: 619 sheet: -1.45 (0.51), residues: 94 loop : -1.63 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 389 TYR 0.017 0.002 TYR A 40 PHE 0.015 0.001 PHE A 779 TRP 0.033 0.002 TRP A 27 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9717) covalent geometry : angle 0.78844 (13247) SS BOND : bond 0.00465 ( 15) SS BOND : angle 1.79283 ( 30) hydrogen bonds : bond 0.04910 ( 494) hydrogen bonds : angle 5.16134 ( 1431) link_BETA1-3 : bond 0.00917 ( 1) link_BETA1-3 : angle 6.20085 ( 3) link_BETA1-4 : bond 0.00586 ( 5) link_BETA1-4 : angle 2.64195 ( 15) link_NAG-ASN : bond 0.00609 ( 13) link_NAG-ASN : angle 3.76411 ( 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 219 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.321 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: 0.8662 (mtm110) cc_final: 0.8367 (ttp-110) REVERT: A 103 ASN cc_start: 0.8723 (m-40) cc_final: 0.8454 (m-40) REVERT: A 156 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6088 (tmm) REVERT: A 222 ASN cc_start: 0.6348 (OUTLIER) cc_final: 0.6011 (m110) REVERT: A 460 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: A 742 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6139 (mt-10) REVERT: A 766 LEU cc_start: 0.8827 (tp) cc_final: 0.8503 (tp) REVERT: A 858 ILE cc_start: 0.9374 (mm) cc_final: 0.8646 (tt) REVERT: A 889 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8891 (t) REVERT: A 909 CYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 991 GLN cc_start: 0.8582 (pt0) cc_final: 0.8302 (pt0) REVERT: A 1026 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7718 (pp) REVERT: A 1106 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8718 (mp) REVERT: A 1114 MET cc_start: 0.8101 (tmm) cc_final: 0.7522 (tmm) REVERT: A 1143 TRP cc_start: 0.7839 (t60) cc_final: 0.7486 (t60) REVERT: A 1175 PHE cc_start: 0.8174 (t80) cc_final: 0.7820 (t80) REVERT: A 1179 MET cc_start: 0.5930 (mtm) cc_final: 0.5663 (ttp) outliers start: 54 outliers final: 33 residues processed: 206 average time/residue: 0.0756 time to fit residues: 22.6874 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN 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 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 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU 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 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 1078 VAL Chi-restraints excluded: chain A residue 1106 LEU 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 1161 CYS 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: 2.9990 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A1008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103107 restraints weight = 17532.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103637 restraints weight = 10365.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104447 restraints weight = 8865.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104893 restraints weight = 6616.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105179 restraints weight = 6242.468| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9751 Z= 0.161 Angle : 0.870 20.832 13334 Z= 0.400 Chirality : 0.057 1.186 1556 Planarity : 0.004 0.037 1660 Dihedral : 13.599 103.302 1802 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.65 % Allowed : 21.36 % Favored : 73.99 % 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: 0.68 (0.21), residues: 619 sheet: -1.34 (0.51), residues: 94 loop : -1.55 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.024 0.002 TYR A 457 PHE 0.018 0.001 PHE A1167 TRP 0.020 0.001 TRP A 27 HIS 0.008 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9717) covalent geometry : angle 0.80528 (13247) SS BOND : bond 0.00374 ( 15) SS BOND : angle 1.84196 ( 30) hydrogen bonds : bond 0.04849 ( 494) hydrogen bonds : angle 5.09672 ( 1431) link_BETA1-3 : bond 0.00656 ( 1) link_BETA1-3 : angle 6.15848 ( 3) link_BETA1-4 : bond 0.00665 ( 5) link_BETA1-4 : angle 2.51066 ( 15) link_NAG-ASN : bond 0.00906 ( 13) link_NAG-ASN : angle 5.53035 ( 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 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8659 (m-40) cc_final: 0.8309 (m-40) REVERT: A 156 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.5986 (tmm) REVERT: A 217 MET cc_start: 0.2034 (mmt) cc_final: 0.1702 (mmt) REVERT: A 222 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.6113 (m110) REVERT: A 460 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: A 488 PHE cc_start: 0.8866 (m-80) cc_final: 0.8610 (m-10) REVERT: A 495 LEU cc_start: 0.9119 (tp) cc_final: 0.8732 (tp) REVERT: A 766 LEU cc_start: 0.8856 (tp) cc_final: 0.8465 (tp) REVERT: A 858 ILE cc_start: 0.9347 (mm) cc_final: 0.8683 (tt) REVERT: A 889 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8893 (t) REVERT: A 909 CYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 991 GLN cc_start: 0.8564 (pt0) cc_final: 0.8307 (pt0) REVERT: A 1026 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7683 (pp) REVERT: A 1114 MET cc_start: 0.8097 (tmm) cc_final: 0.7577 (tmm) REVERT: A 1143 TRP cc_start: 0.7886 (t60) cc_final: 0.7506 (t60) REVERT: A 1175 PHE cc_start: 0.8137 (t80) cc_final: 0.7825 (t80) outliers start: 47 outliers final: 36 residues processed: 202 average time/residue: 0.0822 time to fit residues: 24.0766 Evaluate side-chains 191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP 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 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 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 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 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 973 ASP 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 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: 0.9980 chunk 89 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.134589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105130 restraints weight = 17484.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105817 restraints weight = 9880.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106426 restraints weight = 9180.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107185 restraints weight = 6362.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108905 restraints weight = 5616.307| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9751 Z= 0.143 Angle : 0.840 15.441 13334 Z= 0.385 Chirality : 0.048 0.283 1556 Planarity : 0.005 0.064 1660 Dihedral : 12.511 102.560 1801 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 5.64 % Allowed : 20.38 % Favored : 73.99 % 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: -0.43 (0.25), residues: 1167 helix: 0.74 (0.21), residues: 611 sheet: -1.19 (0.53), residues: 94 loop : -1.46 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 978 TYR 0.018 0.001 TYR A 40 PHE 0.018 0.001 PHE A1167 TRP 0.023 0.001 TRP A 27 HIS 0.008 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9717) covalent geometry : angle 0.78956 (13247) SS BOND : bond 0.00513 ( 15) SS BOND : angle 1.99555 ( 30) hydrogen bonds : bond 0.04589 ( 494) hydrogen bonds : angle 4.99829 ( 1431) link_BETA1-3 : bond 0.00660 ( 1) link_BETA1-3 : angle 5.84441 ( 3) link_BETA1-4 : bond 0.00552 ( 5) link_BETA1-4 : angle 2.36915 ( 15) link_NAG-ASN : bond 0.00743 ( 13) link_NAG-ASN : angle 4.68240 ( 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 215 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8638 (m-40) cc_final: 0.8415 (m-40) REVERT: A 156 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5937 (tmm) REVERT: A 222 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6075 (m110) REVERT: A 457 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6026 (p90) REVERT: A 488 PHE cc_start: 0.8898 (m-80) cc_final: 0.8624 (m-10) REVERT: A 662 LEU cc_start: 0.8124 (mp) cc_final: 0.7830 (mp) REVERT: A 766 LEU cc_start: 0.8788 (tp) cc_final: 0.8469 (tp) REVERT: A 858 ILE cc_start: 0.9332 (mm) cc_final: 0.8672 (tt) REVERT: A 889 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8898 (t) REVERT: A 909 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 944 ASP cc_start: 0.8155 (p0) cc_final: 0.7939 (p0) REVERT: A 991 GLN cc_start: 0.8519 (pt0) cc_final: 0.8296 (pt0) REVERT: A 1026 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7857 (pp) REVERT: A 1114 MET cc_start: 0.7929 (tmm) cc_final: 0.7456 (tmm) REVERT: A 1143 TRP cc_start: 0.7975 (t60) cc_final: 0.7602 (t60) REVERT: A 1175 PHE cc_start: 0.8076 (t80) cc_final: 0.7762 (t80) outliers start: 57 outliers final: 40 residues processed: 202 average time/residue: 0.0757 time to fit residues: 22.8927 Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 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 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 751 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 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN 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 973 ASP 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 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 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: 0.9980 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104154 restraints weight = 17600.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104402 restraints weight = 10499.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105123 restraints weight = 9464.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105618 restraints weight = 6833.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105928 restraints weight = 6475.104| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9751 Z= 0.162 Angle : 0.866 18.585 13334 Z= 0.400 Chirality : 0.048 0.289 1556 Planarity : 0.004 0.036 1660 Dihedral : 12.043 104.086 1798 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 5.14 % Allowed : 21.86 % Favored : 73.00 % 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: -0.35 (0.25), residues: 1167 helix: 0.74 (0.21), residues: 620 sheet: -1.16 (0.54), residues: 94 loop : -1.34 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 978 TYR 0.018 0.001 TYR A 40 PHE 0.026 0.001 PHE A1167 TRP 0.022 0.002 TRP A 27 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9717) covalent geometry : angle 0.81045 (13247) SS BOND : bond 0.00387 ( 15) SS BOND : angle 2.19417 ( 30) hydrogen bonds : bond 0.04698 ( 494) hydrogen bonds : angle 5.01594 ( 1431) link_BETA1-3 : bond 0.00467 ( 1) link_BETA1-3 : angle 5.75878 ( 3) link_BETA1-4 : bond 0.00572 ( 5) link_BETA1-4 : angle 2.31829 ( 15) link_NAG-ASN : bond 0.01118 ( 13) link_NAG-ASN : angle 4.99373 ( 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 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8716 (m-40) cc_final: 0.8472 (m-40) REVERT: A 156 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5975 (tmm) REVERT: A 220 MET cc_start: 0.7617 (tmm) cc_final: 0.7118 (tmm) REVERT: A 222 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.5888 (m110) REVERT: A 488 PHE cc_start: 0.8879 (m-80) cc_final: 0.8656 (m-10) REVERT: A 662 LEU cc_start: 0.8138 (mp) cc_final: 0.7848 (mp) REVERT: A 766 LEU cc_start: 0.8935 (tp) cc_final: 0.8628 (tp) REVERT: A 858 ILE cc_start: 0.9366 (mm) cc_final: 0.8657 (tt) REVERT: A 864 LEU cc_start: 0.7445 (pt) cc_final: 0.6775 (mt) REVERT: A 889 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8924 (t) REVERT: A 909 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8505 (p) REVERT: A 944 ASP cc_start: 0.8122 (p0) cc_final: 0.7831 (p0) REVERT: A 1026 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7870 (pp) REVERT: A 1090 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 1114 MET cc_start: 0.7876 (tmm) cc_final: 0.7373 (tmm) REVERT: A 1143 TRP cc_start: 0.7981 (t60) cc_final: 0.7728 (t60) REVERT: A 1175 PHE cc_start: 0.8083 (t80) cc_final: 0.7783 (t80) outliers start: 52 outliers final: 43 residues processed: 190 average time/residue: 0.0805 time to fit residues: 22.6930 Evaluate side-chains 192 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 88 GLN 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 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 480 THR 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 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 751 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 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 889 VAL 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 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL 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: 1.9990 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.135517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105903 restraints weight = 17553.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105886 restraints weight = 10647.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106988 restraints weight = 8837.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107584 restraints weight = 6506.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108103 restraints weight = 5773.675| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9751 Z= 0.142 Angle : 0.824 19.886 13334 Z= 0.382 Chirality : 0.047 0.299 1556 Planarity : 0.004 0.037 1660 Dihedral : 11.579 103.580 1798 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.49 % Rotamer: Outliers : 5.24 % Allowed : 22.16 % Favored : 72.60 % 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: -0.24 (0.25), residues: 1167 helix: 0.83 (0.21), residues: 612 sheet: -1.14 (0.55), residues: 94 loop : -1.25 (0.30), residues: 461 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 0.027 0.001 PHE A1167 TRP 0.023 0.002 TRP A 27 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9717) covalent geometry : angle 0.76866 (13247) SS BOND : bond 0.00412 ( 15) SS BOND : angle 2.01227 ( 30) hydrogen bonds : bond 0.04526 ( 494) hydrogen bonds : angle 4.96183 ( 1431) link_BETA1-3 : bond 0.00843 ( 1) link_BETA1-3 : angle 5.36883 ( 3) link_BETA1-4 : bond 0.00647 ( 5) link_BETA1-4 : angle 2.31447 ( 15) link_NAG-ASN : bond 0.00789 ( 13) link_NAG-ASN : angle 4.92369 ( 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 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: A 103 ASN cc_start: 0.8727 (m-40) cc_final: 0.8461 (m-40) REVERT: A 156 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5889 (tmm) REVERT: A 220 MET cc_start: 0.7132 (tmm) cc_final: 0.6908 (tmm) REVERT: A 577 LEU cc_start: 0.8502 (mp) cc_final: 0.8294 (tp) REVERT: A 712 ASP cc_start: 0.7896 (t0) cc_final: 0.7641 (t0) REVERT: A 766 LEU cc_start: 0.8871 (tp) cc_final: 0.8569 (tp) REVERT: A 858 ILE cc_start: 0.9336 (mm) cc_final: 0.8647 (tt) REVERT: A 864 LEU cc_start: 0.7402 (pt) cc_final: 0.6820 (mt) REVERT: A 889 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 909 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 944 ASP cc_start: 0.8098 (p0) cc_final: 0.7797 (p0) REVERT: A 1026 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7817 (pp) REVERT: A 1114 MET cc_start: 0.7867 (tmm) cc_final: 0.7327 (tmm) REVERT: A 1143 TRP cc_start: 0.7954 (t60) cc_final: 0.7688 (t60) REVERT: A 1175 PHE cc_start: 0.8031 (t80) cc_final: 0.7793 (t80) REVERT: A 1202 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7784 (mm) outliers start: 53 outliers final: 41 residues processed: 200 average time/residue: 0.0788 time to fit residues: 23.3066 Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 88 GLN Chi-restraints excluded: chain A residue 107 LEU 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 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 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 596 ASN 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 751 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 838 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 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 973 ASP 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 1179 MET Chi-restraints excluded: chain A residue 1202 ILE 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: 0.5980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 14 optimal weight: 0.0020 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106471 restraints weight = 17547.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106370 restraints weight = 10655.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107676 restraints weight = 8574.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108449 restraints weight = 6384.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109743 restraints weight = 6258.477| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4652 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= 0.140 Angle : 0.840 19.886 13334 Z= 0.387 Chirality : 0.047 0.299 1556 Planarity : 0.004 0.037 1660 Dihedral : 11.264 103.377 1798 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 4.65 % Allowed : 23.44 % Favored : 71.91 % 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: -0.20 (0.25), residues: 1167 helix: 0.85 (0.21), residues: 611 sheet: -1.13 (0.56), residues: 94 loop : -1.19 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.035 0.001 TYR A 515 PHE 0.033 0.001 PHE A1110 TRP 0.023 0.002 TRP A 189 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9717) covalent geometry : angle 0.78794 (13247) SS BOND : bond 0.00395 ( 15) SS BOND : angle 1.88585 ( 30) hydrogen bonds : bond 0.04465 ( 494) hydrogen bonds : angle 4.99182 ( 1431) link_BETA1-3 : bond 0.00279 ( 1) link_BETA1-3 : angle 5.09912 ( 3) link_BETA1-4 : bond 0.00734 ( 5) link_BETA1-4 : angle 2.34102 ( 15) link_NAG-ASN : bond 0.00800 ( 13) link_NAG-ASN : angle 4.82642 ( 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 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8793 (m-40) cc_final: 0.8501 (m-40) REVERT: A 156 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5928 (tmm) REVERT: A 222 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.5766 (m110) REVERT: A 528 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 577 LEU cc_start: 0.8483 (mp) cc_final: 0.8266 (tp) REVERT: A 766 LEU cc_start: 0.8832 (tp) cc_final: 0.8535 (tp) REVERT: A 858 ILE cc_start: 0.9334 (mm) cc_final: 0.8636 (tt) REVERT: A 864 LEU cc_start: 0.7384 (pt) cc_final: 0.6818 (mt) REVERT: A 889 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8953 (t) REVERT: A 909 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 944 ASP cc_start: 0.8158 (p0) cc_final: 0.7801 (p0) REVERT: A 1026 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7765 (pp) REVERT: A 1114 MET cc_start: 0.7888 (tmm) cc_final: 0.7350 (tmm) REVERT: A 1143 TRP cc_start: 0.7967 (t60) cc_final: 0.7698 (t60) REVERT: A 1175 PHE cc_start: 0.8037 (t80) cc_final: 0.7783 (t80) REVERT: A 1193 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7023 (t-90) outliers start: 47 outliers final: 38 residues processed: 191 average time/residue: 0.0789 time to fit residues: 22.3880 Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS 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 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 662 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 751 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 838 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 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 973 ASP 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 1179 MET 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 109 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.134436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104875 restraints weight = 17541.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104629 restraints weight = 10631.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105919 restraints weight = 8660.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106408 restraints weight = 6467.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106468 restraints weight = 6348.040| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9751 Z= 0.156 Angle : 0.844 19.722 13334 Z= 0.388 Chirality : 0.047 0.284 1556 Planarity : 0.004 0.036 1660 Dihedral : 11.036 105.347 1798 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 4.65 % Allowed : 23.64 % 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: -0.26 (0.25), residues: 1167 helix: 0.77 (0.21), residues: 621 sheet: -1.31 (0.53), residues: 95 loop : -1.19 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.026 0.001 TYR A 515 PHE 0.029 0.002 PHE A1110 TRP 0.025 0.002 TRP A 189 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9717) covalent geometry : angle 0.79596 (13247) SS BOND : bond 0.00368 ( 15) SS BOND : angle 1.82171 ( 30) hydrogen bonds : bond 0.04626 ( 494) hydrogen bonds : angle 5.01346 ( 1431) link_BETA1-3 : bond 0.00309 ( 1) link_BETA1-3 : angle 4.98253 ( 3) link_BETA1-4 : bond 0.00645 ( 5) link_BETA1-4 : angle 2.22538 ( 15) link_NAG-ASN : bond 0.00762 ( 13) link_NAG-ASN : angle 4.71040 ( 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 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8754 (m-40) cc_final: 0.8455 (m-40) REVERT: A 156 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5872 (tmm) REVERT: A 222 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6045 (m110) REVERT: A 528 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 577 LEU cc_start: 0.8545 (mp) cc_final: 0.8305 (tp) REVERT: A 766 LEU cc_start: 0.8914 (tp) cc_final: 0.8615 (tp) REVERT: A 858 ILE cc_start: 0.9362 (mm) cc_final: 0.8623 (tt) REVERT: A 864 LEU cc_start: 0.7319 (pt) cc_final: 0.6659 (mt) REVERT: A 889 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 944 ASP cc_start: 0.8176 (p0) cc_final: 0.7850 (p0) REVERT: A 1026 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 1114 MET cc_start: 0.7739 (tmm) cc_final: 0.7201 (tmm) REVERT: A 1143 TRP cc_start: 0.7925 (t60) cc_final: 0.7654 (t60) REVERT: A 1175 PHE cc_start: 0.8110 (t80) cc_final: 0.7809 (t80) REVERT: A 1193 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7087 (t-90) outliers start: 47 outliers final: 39 residues processed: 191 average time/residue: 0.0777 time to fit residues: 22.2541 Evaluate side-chains 193 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS 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 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 630 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 751 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 838 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 889 VAL 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 1048 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1179 MET 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: 2.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 94 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.134280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104976 restraints weight = 17589.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104188 restraints weight = 11295.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105722 restraints weight = 9026.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106189 restraints weight = 6406.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106308 restraints weight = 6298.240| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9751 Z= 0.158 Angle : 0.844 19.696 13334 Z= 0.388 Chirality : 0.047 0.276 1556 Planarity : 0.004 0.045 1660 Dihedral : 10.889 105.998 1798 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.65 % Allowed : 23.44 % Favored : 71.91 % 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: -0.27 (0.25), residues: 1167 helix: 0.82 (0.21), residues: 616 sheet: -1.29 (0.53), residues: 94 loop : -1.26 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 978 TYR 0.023 0.001 TYR A 515 PHE 0.028 0.002 PHE A1110 TRP 0.029 0.002 TRP A 189 HIS 0.010 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9717) covalent geometry : angle 0.79647 (13247) SS BOND : bond 0.00404 ( 15) SS BOND : angle 1.94317 ( 30) hydrogen bonds : bond 0.04577 ( 494) hydrogen bonds : angle 5.02204 ( 1431) link_BETA1-3 : bond 0.00342 ( 1) link_BETA1-3 : angle 4.69161 ( 3) link_BETA1-4 : bond 0.00651 ( 5) link_BETA1-4 : angle 2.15775 ( 15) link_NAG-ASN : bond 0.00790 ( 13) link_NAG-ASN : angle 4.66949 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.69 seconds wall clock time: 26 minutes 9.50 seconds (1569.50 seconds total)