Starting phenix.real_space_refine on Tue Dec 31 08:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_21548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_21548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_21548.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_21548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5u_21548/12_2024/6w5u_21548.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'TYR:plan': 1, 'ARG:plan': 1, 'TRP: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: 5.91, per 1000 atoms: 0.62 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 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: 1.03 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: 3.26 Time building geometry restraints manager: 3.15 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- 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 : 0.011 0.135 9717 Z= 0.715 Angle : 1.525 42.080 13247 Z= 0.871 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (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 TRP 0.070 0.005 TRP A1145 HIS 0.010 0.003 HIS A1239 PHE 0.040 0.004 PHE A 339 TYR 0.030 0.003 TYR A 423 ARG 0.007 0.001 ARG A 389 *********************** 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 : 1.009 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: 0.2181 time to fit residues: 83.7338 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 : 1.102 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 447 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS A 530 HIS A 596 ASN A 775 GLN A 793 ASN A1016 HIS A1137 ASN A1239 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9717 Z= 0.281 Angle : 0.938 12.541 13247 Z= 0.450 Chirality : 0.057 0.477 1556 Planarity : 0.005 0.045 1660 Dihedral : 18.178 117.067 1846 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.06 % Rotamer: Outliers : 4.95 % Allowed : 15.03 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1167 helix: 0.02 (0.20), residues: 616 sheet: -1.50 (0.55), residues: 88 loop : -2.01 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 27 HIS 0.007 0.002 HIS A 510 PHE 0.022 0.002 PHE A 998 TYR 0.034 0.002 TYR A 40 ARG 0.009 0.001 ARG A 978 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8785 (p) cc_final: 0.8584 (t) REVERT: A 78 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8290 (ttp-110) REVERT: A 107 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8816 (tp) REVERT: A 111 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 156 MET cc_start: 0.6641 (tmm) cc_final: 0.6330 (tmm) REVERT: A 222 ASN cc_start: 0.5986 (OUTLIER) cc_final: 0.5626 (m110) REVERT: A 460 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: A 714 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7301 (ptt-90) REVERT: A 742 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6392 (mt-10) REVERT: A 766 LEU cc_start: 0.8571 (tp) cc_final: 0.8089 (tp) REVERT: A 857 ASP cc_start: 0.7549 (m-30) cc_final: 0.7340 (m-30) REVERT: A 858 ILE cc_start: 0.9220 (mm) cc_final: 0.8577 (tt) REVERT: A 982 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8185 (tm) REVERT: A 1114 MET cc_start: 0.8285 (tmm) cc_final: 0.7719 (tmm) REVERT: A 1143 TRP cc_start: 0.7950 (t60) cc_final: 0.7519 (t60) REVERT: A 1175 PHE cc_start: 0.8121 (t80) cc_final: 0.7737 (t80) REVERT: A 1179 MET cc_start: 0.6263 (mtm) cc_final: 0.5962 (ttp) REVERT: A 1222 GLN cc_start: 0.7549 (tt0) cc_final: 0.7312 (tm-30) outliers start: 50 outliers final: 27 residues processed: 237 average time/residue: 0.2074 time to fit residues: 69.5318 Evaluate side-chains 189 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 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 714 ARG Chi-restraints excluded: chain A residue 751 LEU 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 1060 LEU Chi-restraints excluded: chain A residue 1078 VAL 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 59 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 489 GLN A1008 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9717 Z= 0.217 Angle : 0.807 9.946 13247 Z= 0.391 Chirality : 0.050 0.343 1556 Planarity : 0.005 0.047 1660 Dihedral : 15.537 103.885 1809 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.00 % Favored : 93.74 % Rotamer: Outliers : 4.15 % Allowed : 17.71 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1167 helix: 0.48 (0.21), residues: 613 sheet: -1.53 (0.49), residues: 95 loop : -1.58 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 27 HIS 0.011 0.001 HIS A 497 PHE 0.017 0.002 PHE A 488 TYR 0.023 0.002 TYR A 40 ARG 0.005 0.001 ARG A 389 *********************** 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 223 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8894 (p) cc_final: 0.8668 (t) REVERT: A 78 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8377 (ttp-110) REVERT: A 103 ASN cc_start: 0.8887 (m-40) cc_final: 0.8559 (m-40) REVERT: A 217 MET cc_start: 0.2019 (mmt) cc_final: 0.1786 (mmt) REVERT: A 222 ASN cc_start: 0.6162 (OUTLIER) cc_final: 0.5821 (m110) REVERT: A 488 PHE cc_start: 0.8944 (m-80) cc_final: 0.8692 (m-10) REVERT: A 504 PHE cc_start: 0.7308 (m-80) cc_final: 0.6800 (m-10) REVERT: A 653 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8152 (mppt) REVERT: A 697 VAL cc_start: 0.7684 (m) cc_final: 0.7479 (t) REVERT: A 714 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7014 (ptt-90) REVERT: A 742 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6203 (mt-10) REVERT: A 766 LEU cc_start: 0.8562 (tp) cc_final: 0.8080 (tp) REVERT: A 857 ASP cc_start: 0.7620 (m-30) cc_final: 0.7322 (m-30) REVERT: A 858 ILE cc_start: 0.9241 (mm) cc_final: 0.8606 (tt) REVERT: A 872 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (mmt) REVERT: A 909 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 1106 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 1114 MET cc_start: 0.8183 (tmm) cc_final: 0.7572 (tmm) REVERT: A 1143 TRP cc_start: 0.7950 (t60) cc_final: 0.7540 (t60) REVERT: A 1175 PHE cc_start: 0.8096 (t80) cc_final: 0.7833 (t80) REVERT: A 1179 MET cc_start: 0.6050 (mtm) cc_final: 0.5750 (ttp) outliers start: 42 outliers final: 28 residues processed: 210 average time/residue: 0.2177 time to fit residues: 65.6762 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 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 702 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 748 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 872 MET Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS 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 1161 CYS Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 0.0670 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9717 Z= 0.262 Angle : 0.803 10.735 13247 Z= 0.386 Chirality : 0.050 0.311 1556 Planarity : 0.005 0.039 1660 Dihedral : 14.246 104.040 1806 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 5.04 % Allowed : 18.89 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1167 helix: 0.56 (0.21), residues: 619 sheet: -1.50 (0.49), residues: 95 loop : -1.55 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 27 HIS 0.009 0.001 HIS A 497 PHE 0.022 0.002 PHE A1110 TYR 0.029 0.002 TYR A 515 ARG 0.003 0.001 ARG A 978 *********************** 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 213 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8938 (p) cc_final: 0.8716 (t) REVERT: A 78 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8344 (ttp-110) REVERT: A 103 ASN cc_start: 0.8788 (m-40) cc_final: 0.8446 (m-40) REVERT: A 156 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6188 (tmm) REVERT: A 222 ASN cc_start: 0.6339 (OUTLIER) cc_final: 0.6096 (m110) REVERT: A 393 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 460 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: A 488 PHE cc_start: 0.9013 (m-80) cc_final: 0.8751 (m-10) REVERT: A 742 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6275 (mt-10) REVERT: A 766 LEU cc_start: 0.8620 (tp) cc_final: 0.8153 (tp) REVERT: A 857 ASP cc_start: 0.7728 (m-30) cc_final: 0.7437 (m-30) REVERT: A 858 ILE cc_start: 0.9348 (mm) cc_final: 0.8767 (tt) REVERT: A 909 CYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 1026 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 1106 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 1114 MET cc_start: 0.8148 (tmm) cc_final: 0.7562 (tmm) REVERT: A 1143 TRP cc_start: 0.7986 (t60) cc_final: 0.7641 (t60) REVERT: A 1175 PHE cc_start: 0.8111 (t80) cc_final: 0.7810 (t80) REVERT: A 1179 MET cc_start: 0.5869 (mtm) cc_final: 0.5586 (ttp) REVERT: A 1193 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7095 (t-90) outliers start: 51 outliers final: 31 residues processed: 201 average time/residue: 0.2067 time to fit residues: 58.8923 Evaluate side-chains 195 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 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 1026 LEU 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 1155 VAL Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9717 Z= 0.195 Angle : 0.783 11.259 13247 Z= 0.373 Chirality : 0.058 1.320 1556 Planarity : 0.004 0.036 1660 Dihedral : 13.089 101.964 1801 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.55 % Allowed : 19.58 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1167 helix: 0.75 (0.21), residues: 610 sheet: -1.35 (0.51), residues: 94 loop : -1.45 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 27 HIS 0.009 0.001 HIS A 497 PHE 0.024 0.001 PHE A 504 TYR 0.023 0.001 TYR A 457 ARG 0.004 0.000 ARG A 714 *********************** 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: 46 poor density : 167 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9039 (p) cc_final: 0.8821 (t) REVERT: A 103 ASN cc_start: 0.8725 (m-40) cc_final: 0.8510 (m-40) REVERT: A 156 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6080 (tmm) REVERT: A 222 ASN cc_start: 0.6525 (OUTLIER) cc_final: 0.6013 (m110) REVERT: A 488 PHE cc_start: 0.8923 (m-80) cc_final: 0.8683 (m-10) REVERT: A 662 LEU cc_start: 0.8162 (mp) cc_final: 0.7841 (mp) REVERT: A 742 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6173 (mt-10) REVERT: A 766 LEU cc_start: 0.8586 (tp) cc_final: 0.8251 (tp) REVERT: A 857 ASP cc_start: 0.7623 (m-30) cc_final: 0.7304 (m-30) REVERT: A 858 ILE cc_start: 0.9278 (mm) cc_final: 0.8713 (tt) REVERT: A 909 CYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 1026 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 1106 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 1114 MET cc_start: 0.8134 (tmm) cc_final: 0.7527 (tmm) REVERT: A 1143 TRP cc_start: 0.7852 (t60) cc_final: 0.7440 (t60) REVERT: A 1175 PHE cc_start: 0.8046 (t80) cc_final: 0.7746 (t80) REVERT: A 1179 MET cc_start: 0.5781 (mtm) cc_final: 0.5464 (ttp) REVERT: A 1193 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7077 (t-90) outliers start: 46 outliers final: 35 residues processed: 202 average time/residue: 0.2020 time to fit residues: 58.7405 Evaluate side-chains 192 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 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 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 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 909 CYS Chi-restraints excluded: chain A residue 1026 LEU 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 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN A1008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 9717 Z= 0.492 Angle : 0.944 11.040 13247 Z= 0.462 Chirality : 0.055 0.318 1556 Planarity : 0.005 0.039 1660 Dihedral : 12.859 108.472 1798 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.29 % Rotamer: Outliers : 5.84 % Allowed : 20.47 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1167 helix: 0.33 (0.21), residues: 605 sheet: -1.77 (0.51), residues: 87 loop : -1.78 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1145 HIS 0.007 0.002 HIS A1042 PHE 0.027 0.003 PHE A 504 TYR 0.023 0.003 TYR A1037 ARG 0.013 0.001 ARG A 96 *********************** 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 207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9119 (p) cc_final: 0.8901 (t) REVERT: A 103 ASN cc_start: 0.8758 (m-40) cc_final: 0.8490 (m-40) REVERT: A 146 TYR cc_start: 0.6642 (t80) cc_final: 0.6429 (t80) REVERT: A 156 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6059 (tmm) REVERT: A 222 ASN cc_start: 0.6388 (OUTLIER) cc_final: 0.5835 (m110) REVERT: A 457 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5953 (p90) REVERT: A 766 LEU cc_start: 0.8820 (tp) cc_final: 0.8592 (tp) REVERT: A 1026 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (pp) REVERT: A 1114 MET cc_start: 0.8033 (tmm) cc_final: 0.7348 (tmm) REVERT: A 1143 TRP cc_start: 0.8039 (t60) cc_final: 0.7600 (t60) REVERT: A 1175 PHE cc_start: 0.8075 (t80) cc_final: 0.7705 (t80) REVERT: A 1193 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7191 (t-90) outliers start: 59 outliers final: 46 residues processed: 193 average time/residue: 0.1978 time to fit residues: 55.0107 Evaluate side-chains 185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 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 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9717 Z= 0.222 Angle : 0.819 13.874 13247 Z= 0.396 Chirality : 0.049 0.297 1556 Planarity : 0.005 0.042 1660 Dihedral : 12.129 104.325 1798 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 5.34 % Allowed : 21.36 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1167 helix: 0.52 (0.21), residues: 617 sheet: -1.37 (0.53), residues: 94 loop : -1.48 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 27 HIS 0.008 0.001 HIS A 497 PHE 0.021 0.002 PHE A 504 TYR 0.019 0.002 TYR A 515 ARG 0.007 0.001 ARG A 978 *********************** 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 222 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8703 (m-40) cc_final: 0.8429 (m-40) REVERT: A 146 TYR cc_start: 0.6580 (t80) cc_final: 0.6350 (t80) REVERT: A 156 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6186 (tmm) REVERT: A 222 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6090 (m110) REVERT: A 742 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6201 (mt-10) REVERT: A 766 LEU cc_start: 0.8619 (tp) cc_final: 0.8295 (tp) REVERT: A 909 CYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 1026 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7929 (pp) REVERT: A 1090 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: A 1114 MET cc_start: 0.8063 (tmm) cc_final: 0.7397 (tmm) REVERT: A 1143 TRP cc_start: 0.7923 (t60) cc_final: 0.7583 (t60) REVERT: A 1175 PHE cc_start: 0.8000 (t80) cc_final: 0.7737 (t80) outliers start: 54 outliers final: 38 residues processed: 207 average time/residue: 0.2006 time to fit residues: 60.4414 Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 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 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 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 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 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 22 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 596 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9717 Z= 0.205 Angle : 0.804 12.345 13247 Z= 0.386 Chirality : 0.047 0.295 1556 Planarity : 0.004 0.037 1660 Dihedral : 11.830 104.291 1798 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 4.75 % Allowed : 22.85 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1167 helix: 0.62 (0.21), residues: 614 sheet: -1.33 (0.54), residues: 94 loop : -1.38 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 27 HIS 0.030 0.002 HIS A1193 PHE 0.025 0.001 PHE A1167 TYR 0.028 0.001 TYR A 515 ARG 0.006 0.000 ARG A 978 *********************** 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 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8803 (m-40) cc_final: 0.8556 (m-40) REVERT: A 156 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6104 (tmm) REVERT: A 217 MET cc_start: 0.1215 (tpp) cc_final: 0.0264 (tpp) REVERT: A 222 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.5938 (m110) REVERT: A 662 LEU cc_start: 0.8086 (mp) cc_final: 0.7799 (mp) REVERT: A 742 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6219 (mt-10) REVERT: A 754 MET cc_start: 0.6696 (ttp) cc_final: 0.6287 (ttt) REVERT: A 766 LEU cc_start: 0.8501 (tp) cc_final: 0.8173 (tp) REVERT: A 909 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 1026 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7862 (pp) REVERT: A 1090 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: A 1114 MET cc_start: 0.8007 (tmm) cc_final: 0.7363 (tmm) REVERT: A 1143 TRP cc_start: 0.7946 (t60) cc_final: 0.7513 (t60) REVERT: A 1175 PHE cc_start: 0.7946 (t80) cc_final: 0.7714 (t80) outliers start: 48 outliers final: 40 residues processed: 185 average time/residue: 0.1995 time to fit residues: 53.2419 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 417 LYS 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 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1179 MET 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 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9717 Z= 0.208 Angle : 0.794 12.167 13247 Z= 0.383 Chirality : 0.047 0.297 1556 Planarity : 0.005 0.053 1660 Dihedral : 11.561 104.140 1798 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 4.75 % Allowed : 23.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1167 helix: 0.68 (0.21), residues: 613 sheet: -1.34 (0.54), residues: 94 loop : -1.32 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 189 HIS 0.008 0.001 HIS A 497 PHE 0.020 0.001 PHE A 488 TYR 0.026 0.001 TYR A 515 ARG 0.005 0.001 ARG A 978 *********************** 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 208 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8414 (mtm110) cc_final: 0.8157 (ttp-110) REVERT: A 103 ASN cc_start: 0.8838 (m-40) cc_final: 0.8587 (m-40) REVERT: A 156 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6160 (tmm) REVERT: A 217 MET cc_start: 0.1216 (tpp) cc_final: 0.0582 (tpp) REVERT: A 528 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 662 LEU cc_start: 0.8217 (mp) cc_final: 0.7921 (mp) REVERT: A 742 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6246 (mt-10) REVERT: A 754 MET cc_start: 0.6676 (ttp) cc_final: 0.6295 (ttt) REVERT: A 766 LEU cc_start: 0.8477 (tp) cc_final: 0.8142 (tp) REVERT: A 909 CYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8495 (p) REVERT: A 1026 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7853 (pp) REVERT: A 1114 MET cc_start: 0.7930 (tmm) cc_final: 0.7279 (tmm) REVERT: A 1143 TRP cc_start: 0.7920 (t60) cc_final: 0.7639 (t60) REVERT: A 1175 PHE cc_start: 0.7976 (t80) cc_final: 0.7726 (t80) outliers start: 48 outliers final: 38 residues processed: 193 average time/residue: 0.2037 time to fit residues: 56.0846 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 : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LYS 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 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1026 LEU 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 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 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9717 Z= 0.206 Angle : 0.800 11.759 13247 Z= 0.381 Chirality : 0.047 0.287 1556 Planarity : 0.005 0.047 1660 Dihedral : 11.270 106.005 1798 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.25 % Allowed : 23.34 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1167 helix: 0.69 (0.21), residues: 607 sheet: -1.33 (0.54), residues: 94 loop : -1.24 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 189 HIS 0.008 0.001 HIS A 497 PHE 0.032 0.001 PHE A1167 TYR 0.023 0.001 TYR A 515 ARG 0.009 0.001 ARG A 978 ********************** 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 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8857 (m-40) cc_final: 0.8554 (m-40) REVERT: A 156 MET cc_start: 0.6645 (tmm) cc_final: 0.6090 (tmm) REVERT: A 217 MET cc_start: 0.1195 (tpp) cc_final: 0.0585 (tpp) REVERT: A 222 ASN cc_start: 0.6605 (OUTLIER) cc_final: 0.5762 (m110) REVERT: A 272 MET cc_start: 0.8768 (mmp) cc_final: 0.8438 (mmp) REVERT: A 528 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 577 LEU cc_start: 0.8484 (mp) cc_final: 0.8258 (tp) REVERT: A 662 LEU cc_start: 0.8210 (mp) cc_final: 0.7930 (mp) REVERT: A 754 MET cc_start: 0.6818 (ttp) cc_final: 0.6460 (ttt) REVERT: A 766 LEU cc_start: 0.8465 (tp) cc_final: 0.8143 (tp) REVERT: A 1026 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7840 (pp) REVERT: A 1114 MET cc_start: 0.7902 (tmm) cc_final: 0.7179 (tmm) REVERT: A 1143 TRP cc_start: 0.7959 (t60) cc_final: 0.7630 (t60) REVERT: A 1175 PHE cc_start: 0.7965 (t80) cc_final: 0.7723 (t80) outliers start: 43 outliers final: 36 residues processed: 188 average time/residue: 0.1953 time to fit residues: 53.2435 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 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 417 LYS 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 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 849 SER 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 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1179 MET 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 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A1008 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104468 restraints weight = 17724.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103364 restraints weight = 11130.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104712 restraints weight = 9617.477| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9717 Z= 0.252 Angle : 0.819 12.229 13247 Z= 0.390 Chirality : 0.048 0.273 1556 Planarity : 0.005 0.042 1660 Dihedral : 11.118 107.100 1798 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 4.25 % Allowed : 23.64 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1167 helix: 0.71 (0.21), residues: 606 sheet: -1.38 (0.54), residues: 95 loop : -1.34 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 189 HIS 0.008 0.001 HIS A 497 PHE 0.026 0.002 PHE A1167 TYR 0.022 0.002 TYR A 515 ARG 0.009 0.001 ARG A 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.49 seconds wall clock time: 38 minutes 56.00 seconds (2336.00 seconds total)