Starting phenix.real_space_refine on Mon Dec 30 09:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5q_33622/12_2024/7y5q_33622_neut.cif" } resolution = 3.8 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 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 114 5.16 5 C 7987 2.51 5 N 2216 2.21 5 O 2444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 28, 'TRANS': 351} Chain breaks: 2 Chain: "B" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8501 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 67, 'TRANS': 1014} Chain breaks: 2 Chain: "C" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.59, per 1000 atoms: 0.59 Number of scatterers: 12762 At special positions: 0 Unit cell: (114.995, 114.995, 139.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 114 16.00 O 2444 8.00 N 2216 7.00 C 7987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A1135 " - pdb=" SG CYS A1189 " distance=2.03 Simple disulfide: pdb=" SG CYS A1147 " - pdb=" SG CYS A1158 " distance=2.03 Simple disulfide: pdb=" SG CYS A1162 " - pdb=" SG CYS A1200 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1249 " distance=2.03 Simple disulfide: pdb=" SG CYS A1220 " - pdb=" SG CYS A1230 " distance=2.03 Simple disulfide: pdb=" SG CYS A1234 " - pdb=" SG CYS A1262 " distance=2.03 Simple disulfide: pdb=" SG CYS A1266 " - pdb=" SG CYS A1319 " distance=2.03 Simple disulfide: pdb=" SG CYS A1282 " - pdb=" SG CYS A1293 " distance=2.03 Simple disulfide: pdb=" SG CYS A1297 " - pdb=" SG CYS A1330 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1378 " distance=2.03 Simple disulfide: pdb=" SG CYS A1348 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1412 " - pdb=" SG CYS A1422 " distance=2.03 Simple disulfide: pdb=" SG CYS A1426 " - pdb=" SG CYS A1474 " distance=2.03 Simple disulfide: pdb=" SG CYS A1478 " - pdb=" SG CYS A1496 " distance=2.03 Simple disulfide: pdb=" SG CYS A1487 " - pdb=" SG CYS A1503 " distance=2.03 Simple disulfide: pdb=" SG CYS A1504 " - pdb=" SG CYS A1528 " distance=2.03 Simple disulfide: pdb=" SG CYS A1520 " - pdb=" SG CYS A1526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 507 " distance=2.04 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS C 120 " distance=2.04 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 701 " distance=2.03 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 880 " - pdb=" SG CYS B 891 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B 910 " distance=2.04 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B 956 " - pdb=" SG CYS B 990 " distance=2.03 Simple disulfide: pdb=" SG CYS B 971 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 197 " - pdb=" SG CYS C 205 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1601 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 486 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 482 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 492 " 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 22 sheets defined 17.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 1279 through 1284 removed outlier: 3.715A pdb=" N ARG A1283 " --> pdb=" O ALA A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 4.221A pdb=" N GLY A1500 " --> pdb=" O CYS A1496 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1501 " --> pdb=" O ASN A1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1496 through 1501' Processing helix chain 'A' and resid 1504 through 1508 Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.683A pdb=" N GLU B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 4.366A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 216' Processing helix chain 'B' and resid 250 through 253 removed outlier: 3.564A pdb=" N ASP B 253 " --> pdb=" O THR B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.736A pdb=" N LEU B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.613A pdb=" N HIS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.634A pdb=" N ARG B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.031A pdb=" N GLY B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 400 through 405 removed outlier: 4.168A pdb=" N THR B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.546A pdb=" N ASN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.591A pdb=" N GLU B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 4.391A pdb=" N GLY B 496 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.703A pdb=" N MET B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 Processing helix chain 'B' and resid 815 through 820 removed outlier: 3.688A pdb=" N SER B 820 " --> pdb=" O MET B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 921 through 925 removed outlier: 3.803A pdb=" N GLN B 924 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 925 " --> pdb=" O PHE B 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 921 through 925' Processing helix chain 'B' and resid 958 through 962 removed outlier: 4.216A pdb=" N ILE B 961 " --> pdb=" O GLY B 958 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 962 " --> pdb=" O TRP B 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 962' Processing helix chain 'B' and resid 993 through 1001 removed outlier: 3.620A pdb=" N GLN B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 96 through 118 Processing helix chain 'C' and resid 124 through 142 removed outlier: 3.690A pdb=" N LYS C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.685A pdb=" N ASN C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 158 removed outlier: 3.900A pdb=" N ILE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 182 through 201 removed outlier: 3.615A pdb=" N GLU C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 removed outlier: 3.801A pdb=" N SER C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AA2, first strand: chain 'A' and resid 1169 through 1172 Processing sheet with id=AA3, first strand: chain 'A' and resid 1189 through 1190 Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1219 removed outlier: 3.592A pdb=" N SER A1231 " --> pdb=" O SER A1219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1238 through 1241 removed outlier: 3.603A pdb=" N LYS A1241 " --> pdb=" O LEU A1261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1275 through 1277 Processing sheet with id=AA7, first strand: chain 'A' and resid 1301 through 1302 Processing sheet with id=AA8, first strand: chain 'A' and resid 1431 through 1435 Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.983A pdb=" N LEU B 130 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR B 139 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 128 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.983A pdb=" N LEU B 130 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR B 139 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 128 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 227 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.742A pdb=" N TRP B 73 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 59 " --> pdb=" O TRP B 73 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 75 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 160 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 311 through 321 removed outlier: 3.692A pdb=" N VAL B 277 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE B 437 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU B 280 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AB5, first strand: chain 'B' and resid 600 through 604 removed outlier: 4.960A pdb=" N VAL B 601 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B 612 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 603 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 609 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP B 830 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 640 through 642 removed outlier: 3.689A pdb=" N GLN B 641 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU B 783 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP B 719 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA B 787 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 717 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 789 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 715 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 791 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 645 through 647 removed outlier: 6.197A pdb=" N TYR B 771 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 690 through 691 removed outlier: 4.006A pdb=" N ILE C 121 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 805 through 810 Processing sheet with id=AC1, first strand: chain 'B' and resid 902 through 903 Processing sheet with id=AC2, first strand: chain 'B' and resid 939 through 943 removed outlier: 4.045A pdb=" N ILE B1020 " --> pdb=" O ALA B1097 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 948 through 949 Processing sheet with id=AC4, first strand: chain 'B' and resid 948 through 949 318 hydrogen bonds defined for protein. 846 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: 5.33 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4112 1.34 - 1.46: 2628 1.46 - 1.58: 6209 1.58 - 1.70: 0 1.70 - 1.82: 139 Bond restraints: 13088 Sorted by residual: bond pdb=" N ASN B1062 " pdb=" CA ASN B1062 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.04e-02 9.25e+03 1.04e+01 bond pdb=" N HIS A1236 " pdb=" CA HIS A1236 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.00e+01 bond pdb=" N PHE A1516 " pdb=" CA PHE A1516 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.62e+00 bond pdb=" N ILE C 160 " pdb=" CA ILE C 160 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.19e+00 bond pdb=" N CYS A1520 " pdb=" CA CYS A1520 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.31e-02 5.83e+03 8.16e+00 ... (remaining 13083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 17264 1.77 - 3.54: 464 3.54 - 5.31: 51 5.31 - 7.08: 9 7.08 - 8.85: 8 Bond angle restraints: 17796 Sorted by residual: angle pdb=" N TRP A1465 " pdb=" CA TRP A1465 " pdb=" C TRP A1465 " ideal model delta sigma weight residual 112.88 106.11 6.77 1.29e+00 6.01e-01 2.75e+01 angle pdb=" N LEU C 45 " pdb=" CA LEU C 45 " pdb=" C LEU C 45 " ideal model delta sigma weight residual 113.02 107.88 5.14 1.20e+00 6.94e-01 1.83e+01 angle pdb=" N ASN B1061 " pdb=" CA ASN B1061 " pdb=" C ASN B1061 " ideal model delta sigma weight residual 111.55 105.70 5.85 1.37e+00 5.33e-01 1.82e+01 angle pdb=" N GLU C 158 " pdb=" CA GLU C 158 " pdb=" C GLU C 158 " ideal model delta sigma weight residual 112.93 108.40 4.53 1.12e+00 7.97e-01 1.64e+01 angle pdb=" CA TYR A1466 " pdb=" C TYR A1466 " pdb=" N PRO A1467 " ideal model delta sigma weight residual 117.60 122.26 -4.66 1.18e+00 7.18e-01 1.56e+01 ... (remaining 17791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7186 17.92 - 35.84: 603 35.84 - 53.76: 118 53.76 - 71.68: 21 71.68 - 89.59: 5 Dihedral angle restraints: 7933 sinusoidal: 3205 harmonic: 4728 Sorted by residual: dihedral pdb=" CB CYS C 109 " pdb=" SG CYS C 109 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 159.33 -66.33 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS B 956 " pdb=" SG CYS B 956 " pdb=" SG CYS B 990 " pdb=" CB CYS B 990 " ideal model delta sinusoidal sigma weight residual 93.00 150.97 -57.97 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS B 867 " pdb=" SG CYS B 867 " pdb=" SG CYS B 895 " pdb=" CB CYS B 895 " ideal model delta sinusoidal sigma weight residual -86.00 -142.60 56.60 1 1.00e+01 1.00e-02 4.32e+01 ... (remaining 7930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1590 0.064 - 0.128: 298 0.128 - 0.192: 32 0.192 - 0.256: 3 0.256 - 0.319: 3 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA TYR A1466 " pdb=" N TYR A1466 " pdb=" C TYR A1466 " pdb=" CB TYR A1466 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHE A1516 " pdb=" N PHE A1516 " pdb=" C PHE A1516 " pdb=" CB PHE A1516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU A1463 " pdb=" N LEU A1463 " pdb=" C LEU A1463 " pdb=" CB LEU A1463 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1923 not shown) Planarity restraints: 2346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B1060 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C ARG B1060 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG B1060 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN B1061 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1234 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C CYS A1234 " -0.039 2.00e-02 2.50e+03 pdb=" O CYS A1234 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A1235 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 687 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO B 688 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 688 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 688 " -0.031 5.00e-02 4.00e+02 ... (remaining 2343 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4020 2.83 - 3.35: 10557 3.35 - 3.87: 20341 3.87 - 4.38: 22501 4.38 - 4.90: 39879 Nonbonded interactions: 97298 Sorted by model distance: nonbonded pdb=" O GLY A1501 " pdb=" OG1 THR A1507 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP B 830 " pdb=" OH TYR B 841 " model vdw 2.316 3.040 nonbonded pdb=" OG SER B 675 " pdb=" OE2 GLU B 783 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR B 541 " pdb=" O PHE B 544 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR A1320 " pdb=" O SER A1324 " model vdw 2.331 3.040 ... (remaining 97293 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.005 0.049 13088 Z= 0.300 Angle : 0.681 8.855 17796 Z= 0.400 Chirality : 0.051 0.319 1926 Planarity : 0.006 0.057 2346 Dihedral : 13.443 89.594 4759 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.70 % Allowed : 8.09 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1620 helix: -2.78 (0.23), residues: 248 sheet: -0.66 (0.32), residues: 296 loop : -1.33 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.004 0.001 HIS B 78 PHE 0.021 0.002 PHE B 912 TYR 0.013 0.002 TYR B 169 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 199 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 ARG cc_start: 0.6819 (mpt-90) cc_final: 0.6025 (mmt-90) REVERT: A 1169 GLN cc_start: 0.7498 (mp10) cc_final: 0.7134 (mm-40) REVERT: A 1466 TYR cc_start: 0.2577 (OUTLIER) cc_final: 0.2338 (m-80) REVERT: A 1479 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5909 (tp30) REVERT: B 71 ARG cc_start: 0.9030 (mmt180) cc_final: 0.8691 (mmt180) REVERT: B 112 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8076 (mm) REVERT: B 174 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: B 246 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 293 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: B 407 ASP cc_start: 0.6874 (m-30) cc_final: 0.6577 (m-30) REVERT: B 479 THR cc_start: 0.9042 (t) cc_final: 0.8758 (m) REVERT: B 481 ILE cc_start: 0.9155 (mm) cc_final: 0.8955 (mm) REVERT: B 959 TRP cc_start: 0.6820 (p-90) cc_final: 0.6493 (p-90) REVERT: B 988 TYR cc_start: 0.7529 (p90) cc_final: 0.7210 (p90) REVERT: C 47 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4227 (tp) REVERT: C 210 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.4632 (t80) outliers start: 96 outliers final: 34 residues processed: 271 average time/residue: 0.2446 time to fit residues: 97.7390 Evaluate side-chains 191 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1466 TYR Chi-restraints excluded: chain A residue 1479 GLU Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 727 TRP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 ASN A1236 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 232 ASN B 294 GLN B 298 GLN ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 834 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13088 Z= 0.244 Angle : 0.567 7.354 17796 Z= 0.301 Chirality : 0.044 0.175 1926 Planarity : 0.005 0.043 2346 Dihedral : 7.747 59.874 1814 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.61 % Allowed : 12.98 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1620 helix: -1.59 (0.30), residues: 246 sheet: -0.71 (0.30), residues: 313 loop : -1.05 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 179 HIS 0.006 0.001 HIS B 78 PHE 0.017 0.002 PHE B 91 TYR 0.014 0.001 TYR A1498 ARG 0.006 0.000 ARG A1456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1169 GLN cc_start: 0.7467 (mp10) cc_final: 0.7029 (mm-40) REVERT: A 1384 TRP cc_start: 0.3475 (OUTLIER) cc_final: 0.3095 (m-90) REVERT: A 1479 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5899 (tp30) REVERT: B 112 LEU cc_start: 0.8354 (mm) cc_final: 0.8144 (mm) REVERT: B 246 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7316 (mm) REVERT: B 256 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 407 ASP cc_start: 0.7012 (m-30) cc_final: 0.6647 (m-30) REVERT: B 412 HIS cc_start: 0.5540 (OUTLIER) cc_final: 0.5099 (p90) REVERT: B 479 THR cc_start: 0.9019 (t) cc_final: 0.8770 (m) REVERT: B 481 ILE cc_start: 0.9268 (mm) cc_final: 0.9009 (mm) REVERT: B 959 TRP cc_start: 0.6988 (p-90) cc_final: 0.6589 (p-90) REVERT: B 988 TYR cc_start: 0.7514 (p90) cc_final: 0.7230 (p90) REVERT: B 1078 HIS cc_start: 0.6240 (OUTLIER) cc_final: 0.5082 (m-70) REVERT: C 47 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.4219 (tp) REVERT: C 179 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6534 (pt) REVERT: C 194 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5322 (mp10) REVERT: C 210 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.4600 (t80) outliers start: 66 outliers final: 34 residues processed: 214 average time/residue: 0.2539 time to fit residues: 81.4656 Evaluate side-chains 185 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1479 GLU Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 727 TRP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1302 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS B 570 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13088 Z= 0.207 Angle : 0.534 8.054 17796 Z= 0.278 Chirality : 0.043 0.174 1926 Planarity : 0.004 0.039 2346 Dihedral : 6.777 58.237 1791 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.33 % Allowed : 14.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1620 helix: -0.99 (0.32), residues: 248 sheet: -0.83 (0.29), residues: 317 loop : -0.97 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 179 HIS 0.005 0.001 HIS B 78 PHE 0.021 0.002 PHE B1010 TYR 0.023 0.001 TYR B 558 ARG 0.002 0.000 ARG A1456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1169 GLN cc_start: 0.7387 (mp10) cc_final: 0.7093 (mm-40) REVERT: A 1384 TRP cc_start: 0.3430 (OUTLIER) cc_final: 0.3033 (m-90) REVERT: A 1455 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6781 (tm-30) REVERT: A 1479 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5836 (tp30) REVERT: B 112 LEU cc_start: 0.8336 (mm) cc_final: 0.8133 (mm) REVERT: B 246 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7235 (mm) REVERT: B 407 ASP cc_start: 0.7102 (m-30) cc_final: 0.6886 (m-30) REVERT: B 412 HIS cc_start: 0.5618 (OUTLIER) cc_final: 0.5163 (p90) REVERT: B 479 THR cc_start: 0.9096 (t) cc_final: 0.8836 (m) REVERT: B 481 ILE cc_start: 0.9268 (mm) cc_final: 0.9031 (mm) REVERT: B 788 MET cc_start: 0.8573 (ttm) cc_final: 0.8279 (ttp) REVERT: B 834 ASN cc_start: 0.7170 (t0) cc_final: 0.6394 (m110) REVERT: B 959 TRP cc_start: 0.7015 (p-90) cc_final: 0.6367 (p-90) REVERT: B 988 TYR cc_start: 0.7539 (p90) cc_final: 0.7260 (p90) REVERT: B 1078 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5004 (m-70) REVERT: C 47 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.4173 (tp) REVERT: C 179 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6472 (pt) REVERT: C 194 GLN cc_start: 0.5442 (OUTLIER) cc_final: 0.5201 (mm-40) REVERT: C 210 PHE cc_start: 0.4924 (OUTLIER) cc_final: 0.4616 (t80) outliers start: 62 outliers final: 39 residues processed: 205 average time/residue: 0.2378 time to fit residues: 73.0297 Evaluate side-chains 191 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1479 GLU Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 727 TRP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13088 Z= 0.211 Angle : 0.527 7.210 17796 Z= 0.272 Chirality : 0.043 0.182 1926 Planarity : 0.004 0.038 2346 Dihedral : 6.495 58.153 1788 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.95 % Allowed : 14.72 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1620 helix: -0.68 (0.33), residues: 248 sheet: -0.90 (0.29), residues: 309 loop : -0.85 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 179 HIS 0.005 0.001 HIS B 78 PHE 0.015 0.001 PHE B 912 TYR 0.013 0.001 TYR B 776 ARG 0.005 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 GLN cc_start: 0.7344 (mp10) cc_final: 0.6899 (mm-40) REVERT: A 1384 TRP cc_start: 0.3377 (OUTLIER) cc_final: 0.3014 (m-90) REVERT: A 1455 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6783 (tm-30) REVERT: A 1479 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5811 (tp30) REVERT: B 112 LEU cc_start: 0.8359 (mm) cc_final: 0.7969 (mt) REVERT: B 407 ASP cc_start: 0.7125 (m-30) cc_final: 0.6917 (m-30) REVERT: B 412 HIS cc_start: 0.5640 (OUTLIER) cc_final: 0.5154 (p90) REVERT: B 479 THR cc_start: 0.9116 (t) cc_final: 0.8862 (m) REVERT: B 481 ILE cc_start: 0.9296 (mm) cc_final: 0.9064 (mm) REVERT: B 530 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7348 (mmmt) REVERT: B 788 MET cc_start: 0.8562 (ttm) cc_final: 0.8265 (ttp) REVERT: B 959 TRP cc_start: 0.7005 (p-90) cc_final: 0.6213 (p-90) REVERT: B 962 ILE cc_start: 0.8749 (mm) cc_final: 0.8237 (mm) REVERT: B 988 TYR cc_start: 0.7565 (p90) cc_final: 0.7278 (p90) REVERT: B 1078 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5003 (m-70) REVERT: C 47 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.3936 (tm) REVERT: C 179 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6447 (pt) outliers start: 71 outliers final: 45 residues processed: 206 average time/residue: 0.2419 time to fit residues: 75.7435 Evaluate side-chains 191 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1479 GLU Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS B 752 ASN ** B1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13088 Z= 0.427 Angle : 0.645 9.643 17796 Z= 0.338 Chirality : 0.047 0.297 1926 Planarity : 0.005 0.041 2346 Dihedral : 6.720 59.811 1780 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.30 % Allowed : 15.63 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1620 helix: -1.01 (0.32), residues: 236 sheet: -1.10 (0.30), residues: 303 loop : -1.05 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 179 HIS 0.008 0.001 HIS B 492 PHE 0.026 0.002 PHE B 91 TYR 0.015 0.002 TYR B 491 ARG 0.004 0.000 ARG B 972 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1193 LYS cc_start: 0.7105 (mmtm) cc_final: 0.6847 (mmtp) REVERT: A 1384 TRP cc_start: 0.3460 (OUTLIER) cc_final: 0.2939 (m-90) REVERT: A 1455 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 112 LEU cc_start: 0.8377 (mm) cc_final: 0.8000 (mt) REVERT: B 407 ASP cc_start: 0.7158 (m-30) cc_final: 0.6943 (m-30) REVERT: B 412 HIS cc_start: 0.5828 (OUTLIER) cc_final: 0.5302 (p90) REVERT: B 481 ILE cc_start: 0.9296 (mm) cc_final: 0.9056 (mm) REVERT: C 47 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.4144 (tm) REVERT: C 179 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6532 (pt) REVERT: C 194 GLN cc_start: 0.5630 (OUTLIER) cc_final: 0.5368 (mm-40) REVERT: C 210 PHE cc_start: 0.5155 (OUTLIER) cc_final: 0.4795 (t80) outliers start: 76 outliers final: 58 residues processed: 211 average time/residue: 0.2354 time to fit residues: 75.0159 Evaluate side-chains 205 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 141 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1274 ASN Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 834 ASN Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 GLN C 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13088 Z= 0.196 Angle : 0.548 12.606 17796 Z= 0.285 Chirality : 0.043 0.256 1926 Planarity : 0.004 0.038 2346 Dihedral : 6.190 57.146 1777 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.33 % Allowed : 17.31 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1620 helix: -0.65 (0.34), residues: 236 sheet: -0.98 (0.30), residues: 304 loop : -0.85 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 959 HIS 0.005 0.001 HIS B 78 PHE 0.013 0.001 PHE B1010 TYR 0.013 0.001 TYR B 776 ARG 0.002 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1384 TRP cc_start: 0.3458 (OUTLIER) cc_final: 0.3058 (m-90) REVERT: B 112 LEU cc_start: 0.8386 (mm) cc_final: 0.8169 (mm) REVERT: B 285 HIS cc_start: 0.5471 (t70) cc_final: 0.4986 (t-90) REVERT: B 407 ASP cc_start: 0.7155 (m-30) cc_final: 0.6952 (m-30) REVERT: B 412 HIS cc_start: 0.5591 (OUTLIER) cc_final: 0.5159 (p90) REVERT: B 481 ILE cc_start: 0.9274 (mm) cc_final: 0.9068 (mm) REVERT: B 959 TRP cc_start: 0.7001 (p-90) cc_final: 0.6683 (p-90) REVERT: B 1078 HIS cc_start: 0.6165 (OUTLIER) cc_final: 0.4956 (m-70) REVERT: C 47 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4140 (tm) REVERT: C 109 CYS cc_start: 0.4410 (t) cc_final: 0.4126 (t) REVERT: C 179 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6376 (pt) REVERT: C 210 PHE cc_start: 0.4982 (OUTLIER) cc_final: 0.4578 (t80) outliers start: 62 outliers final: 43 residues processed: 201 average time/residue: 0.2297 time to fit residues: 70.1039 Evaluate side-chains 187 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 157 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13088 Z= 0.175 Angle : 0.530 10.937 17796 Z= 0.275 Chirality : 0.043 0.239 1926 Planarity : 0.004 0.037 2346 Dihedral : 5.959 56.778 1773 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.33 % Allowed : 17.86 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1620 helix: -0.55 (0.34), residues: 242 sheet: -0.82 (0.30), residues: 307 loop : -0.79 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 179 HIS 0.007 0.001 HIS B 195 PHE 0.026 0.001 PHE B 236 TYR 0.013 0.001 TYR B 776 ARG 0.003 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1384 TRP cc_start: 0.3487 (OUTLIER) cc_final: 0.3119 (m-90) REVERT: B 14 SER cc_start: 0.7415 (t) cc_final: 0.7064 (p) REVERT: B 112 LEU cc_start: 0.8365 (mm) cc_final: 0.8103 (mt) REVERT: B 285 HIS cc_start: 0.5275 (t70) cc_final: 0.4734 (t-90) REVERT: B 412 HIS cc_start: 0.5623 (OUTLIER) cc_final: 0.5186 (p90) REVERT: B 481 ILE cc_start: 0.9276 (mm) cc_final: 0.9064 (mm) REVERT: B 530 LYS cc_start: 0.7535 (mptt) cc_final: 0.7113 (tptp) REVERT: B 1078 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5110 (m-70) REVERT: C 47 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4257 (tm) REVERT: C 179 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6325 (pt) REVERT: C 194 GLN cc_start: 0.5394 (OUTLIER) cc_final: 0.5099 (mm-40) REVERT: C 210 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.4919 (t80) outliers start: 62 outliers final: 45 residues processed: 204 average time/residue: 0.2305 time to fit residues: 71.5772 Evaluate side-chains 190 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1529 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 0.0770 chunk 150 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13088 Z= 0.183 Angle : 0.540 12.918 17796 Z= 0.280 Chirality : 0.043 0.226 1926 Planarity : 0.004 0.037 2346 Dihedral : 5.877 56.891 1771 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.98 % Allowed : 18.21 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1620 helix: -0.50 (0.34), residues: 242 sheet: -0.74 (0.30), residues: 301 loop : -0.76 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 959 HIS 0.019 0.001 HIS B 175 PHE 0.013 0.001 PHE B 912 TYR 0.014 0.001 TYR B 776 ARG 0.002 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1384 TRP cc_start: 0.3446 (OUTLIER) cc_final: 0.3132 (m-90) REVERT: A 1482 MET cc_start: 0.6580 (mmm) cc_final: 0.6322 (mmp) REVERT: B 14 SER cc_start: 0.7392 (t) cc_final: 0.6950 (p) REVERT: B 112 LEU cc_start: 0.8325 (mm) cc_final: 0.8064 (mt) REVERT: B 285 HIS cc_start: 0.5154 (t70) cc_final: 0.4681 (t-90) REVERT: B 412 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5190 (p90) REVERT: B 473 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6848 (ttt) REVERT: B 530 LYS cc_start: 0.7541 (mptt) cc_final: 0.7114 (tptp) REVERT: B 1078 HIS cc_start: 0.6106 (OUTLIER) cc_final: 0.5057 (m-70) REVERT: C 47 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4478 (tm) REVERT: C 109 CYS cc_start: 0.4216 (t) cc_final: 0.3938 (t) REVERT: C 179 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6316 (pt) REVERT: C 194 GLN cc_start: 0.5300 (OUTLIER) cc_final: 0.5007 (mm-40) REVERT: C 210 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4941 (t80) outliers start: 57 outliers final: 42 residues processed: 196 average time/residue: 0.2346 time to fit residues: 70.2434 Evaluate side-chains 194 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13088 Z= 0.199 Angle : 0.542 12.494 17796 Z= 0.281 Chirality : 0.043 0.204 1926 Planarity : 0.004 0.036 2346 Dihedral : 5.778 56.810 1769 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.84 % Allowed : 18.42 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1620 helix: -0.44 (0.34), residues: 241 sheet: -0.71 (0.30), residues: 301 loop : -0.76 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 959 HIS 0.026 0.001 HIS B 175 PHE 0.014 0.001 PHE B 912 TYR 0.014 0.001 TYR B 776 ARG 0.002 0.000 ARG B 909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1384 TRP cc_start: 0.3512 (OUTLIER) cc_final: 0.3196 (m-90) REVERT: B 14 SER cc_start: 0.7351 (t) cc_final: 0.6974 (p) REVERT: B 112 LEU cc_start: 0.8348 (mm) cc_final: 0.8078 (mt) REVERT: B 285 HIS cc_start: 0.5118 (t70) cc_final: 0.4648 (t-90) REVERT: B 309 TYR cc_start: 0.8951 (m-10) cc_final: 0.8602 (m-10) REVERT: B 412 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5178 (p90) REVERT: B 473 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6791 (ttt) REVERT: B 530 LYS cc_start: 0.7492 (mptt) cc_final: 0.7104 (tptp) REVERT: B 565 ASP cc_start: 0.6816 (t0) cc_final: 0.6545 (t0) REVERT: B 1078 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5073 (m-70) REVERT: C 179 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6301 (pt) REVERT: C 194 GLN cc_start: 0.5309 (OUTLIER) cc_final: 0.4961 (mm-40) REVERT: C 210 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.4955 (t80) outliers start: 55 outliers final: 42 residues processed: 195 average time/residue: 0.2397 time to fit residues: 69.7794 Evaluate side-chains 194 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1195 ASN Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13088 Z= 0.185 Angle : 0.541 11.795 17796 Z= 0.280 Chirality : 0.043 0.195 1926 Planarity : 0.004 0.039 2346 Dihedral : 5.639 56.433 1767 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.56 % Allowed : 18.70 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1620 helix: -0.41 (0.34), residues: 243 sheet: -0.68 (0.30), residues: 301 loop : -0.73 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP B 959 HIS 0.024 0.001 HIS B 175 PHE 0.013 0.001 PHE B 912 TYR 0.014 0.001 TYR B 776 ARG 0.007 0.000 ARG B 896 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1384 TRP cc_start: 0.3466 (OUTLIER) cc_final: 0.3167 (m-90) REVERT: B 14 SER cc_start: 0.7406 (t) cc_final: 0.6987 (p) REVERT: B 112 LEU cc_start: 0.8320 (mm) cc_final: 0.8106 (mt) REVERT: B 174 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 285 HIS cc_start: 0.5140 (t70) cc_final: 0.4664 (t-90) REVERT: B 309 TYR cc_start: 0.8982 (m-10) cc_final: 0.8613 (m-10) REVERT: B 412 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.5174 (p90) REVERT: B 473 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6769 (ttt) REVERT: B 530 LYS cc_start: 0.7538 (mptt) cc_final: 0.7112 (tptp) REVERT: B 565 ASP cc_start: 0.6757 (t0) cc_final: 0.6498 (t0) REVERT: B 1078 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.5066 (m-70) REVERT: C 179 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6254 (pt) REVERT: C 194 GLN cc_start: 0.5291 (OUTLIER) cc_final: 0.4943 (mm-40) REVERT: C 210 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.4890 (t80) outliers start: 51 outliers final: 41 residues processed: 197 average time/residue: 0.2436 time to fit residues: 72.2444 Evaluate side-chains 195 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1195 ASN Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1282 CYS Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1384 TRP Chi-restraints excluded: chain A residue 1412 CYS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1476 LYS Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 0.0270 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1236 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 492 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 = 0.3857 r_free = 0.3857 target = 0.166724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142757 restraints weight = 16802.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138736 restraints weight = 25951.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137126 restraints weight = 26903.495| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13088 Z= 0.302 Angle : 0.592 12.279 17796 Z= 0.309 Chirality : 0.045 0.199 1926 Planarity : 0.004 0.038 2346 Dihedral : 5.991 58.011 1767 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.56 % Allowed : 19.05 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1620 helix: -0.55 (0.34), residues: 241 sheet: -0.81 (0.30), residues: 309 loop : -0.82 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP B 959 HIS 0.024 0.001 HIS B 175 PHE 0.020 0.002 PHE B 912 TYR 0.015 0.001 TYR B 776 ARG 0.006 0.000 ARG B 896 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.10 seconds wall clock time: 49 minutes 30.04 seconds (2970.04 seconds total)