Starting phenix.real_space_refine on Thu Feb 15 16:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn1_4281/02_2024/6fn1_4281_updated.pdb" } resolution = 3.58 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 8174 2.51 5 N 2128 2.21 5 O 2383 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12739 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9186 Classifications: {'peptide': 1182} Link IDs: {'CIS': 4, 'PTRANS': 27, 'TRANS': 1150} Chain breaks: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} bond proxies already assigned to first conformer: 1747 Chain: "C" Number of atoms: 1720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} bond proxies already assigned to first conformer: 1763 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'NAG': 3, 'ZQU': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.21, per 1000 atoms: 0.64 Number of scatterers: 12739 At special positions: 0 Unit cell: (96.6, 93.24, 206.64, 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) S 50 16.00 F 4 9.00 O 2383 8.00 N 2128 7.00 C 8174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A1203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG ACYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG BCYS B 200 " distance=2.05 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG ACYS C 204 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG BCYS C 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 93 " " NAG A1303 " - " ASN A 98 " Time building additional restraints: 4.46 Conformation dependent library (CDL) restraints added in 2.9 seconds 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 12 sheets defined 45.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.775A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 87 Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.359A pdb=" N LEU A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 155 removed outlier: 3.848A pdb=" N TYR A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.651A pdb=" N ASP A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 167 through 185 removed outlier: 4.168A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 209 removed outlier: 4.134A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 236 removed outlier: 4.109A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 260 through 263 No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 269 through 320 removed outlier: 4.096A pdb=" N GLU A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 369 removed outlier: 3.845A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Proline residue: A 349 - end of helix removed outlier: 4.147A pdb=" N GLU A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 removed outlier: 4.186A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 532 through 545 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'A' and resid 707 through 738 removed outlier: 4.181A pdb=" N ILE A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.649A pdb=" N SER A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 797 removed outlier: 3.756A pdb=" N THR A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 810 through 822 removed outlier: 4.010A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 852 removed outlier: 3.965A pdb=" N SER A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 878 removed outlier: 3.529A pdb=" N ILE A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Proline residue: A 865 - end of helix removed outlier: 3.741A pdb=" N ALA A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 912 through 965 Proline residue: A 926 - end of helix removed outlier: 3.896A pdb=" N HIS A 935 " --> pdb=" O MET A 931 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 Processing helix chain 'A' and resid 998 through 1010 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1141 through 1150 removed outlier: 3.792A pdb=" N VAL A1145 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 4.092A pdb=" N SER A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1210 through 1220 Processing helix chain 'A' and resid 1256 through 1261 Processing helix chain 'A' and resid 1265 through 1272 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.994A pdb=" N GLU B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing sheet with id= A, first strand: chain 'A' and resid 449 through 452 removed outlier: 5.078A pdb=" N LEU A 412 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 596 through 600 removed outlier: 6.308A pdb=" N THR A 581 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 424 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 583 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N GLY A 426 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1057 through 1059 Processing sheet with id= D, first strand: chain 'A' and resid 1241 through 1245 removed outlier: 6.260A pdb=" N THR A1226 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A1067 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1228 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY A1069 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP A1199 " --> pdb=" O GLY A1113 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL A1115 " --> pdb=" O ASP A1199 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.712A pdb=" N SER B 68 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 94 removed outlier: 5.876A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 120 through 124 removed outlier: 5.865A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 150 through 156 Processing sheet with id= I, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.994A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 129 through 133 Processing sheet with id= L, first strand: chain 'C' and resid 159 through 163 642 hydrogen bonds defined for protein. 1843 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: 4.36 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2067 1.31 - 1.45: 3723 1.45 - 1.59: 7139 1.59 - 1.74: 0 1.74 - 1.88: 85 Bond restraints: 13014 Sorted by residual: bond pdb=" C06 ZQU A1305 " pdb=" C08 ZQU A1305 " ideal model delta sigma weight residual 1.662 1.526 0.136 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C06 ZQU A1304 " pdb=" C08 ZQU A1304 " ideal model delta sigma weight residual 1.662 1.531 0.131 2.00e-02 2.50e+03 4.28e+01 ... (remaining 13009 not shown) Histogram of bond angle deviations from ideal: 59.60 - 75.43: 6 75.43 - 91.27: 0 91.27 - 107.10: 395 107.10 - 122.93: 16330 122.93 - 138.77: 914 Bond angle restraints: 17645 Sorted by residual: angle pdb=" C03 ZQU A1304 " pdb=" C01 ZQU A1304 " pdb=" C04 ZQU A1304 " ideal model delta sigma weight residual 58.20 117.17 -58.97 3.00e+00 1.11e-01 3.86e+02 angle pdb=" C03 ZQU A1305 " pdb=" C01 ZQU A1305 " pdb=" C04 ZQU A1305 " ideal model delta sigma weight residual 58.20 117.08 -58.88 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C SER A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta sigma weight residual 121.70 135.87 -14.17 1.80e+00 3.09e-01 6.20e+01 angle pdb=" C ASN A 370 " pdb=" N LYS A 371 " pdb=" CA LYS A 371 " ideal model delta sigma weight residual 121.70 133.65 -11.95 1.80e+00 3.09e-01 4.41e+01 angle pdb=" C03 ZQU A1305 " pdb=" C02 ZQU A1305 " pdb=" C05 ZQU A1305 " ideal model delta sigma weight residual 138.97 119.49 19.48 3.00e+00 1.11e-01 4.22e+01 ... (remaining 17640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 7438 22.49 - 44.98: 294 44.98 - 67.47: 24 67.47 - 89.96: 6 89.96 - 112.45: 2 Dihedral angle restraints: 7764 sinusoidal: 3078 harmonic: 4686 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 109.15 70.85 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual 180.00 -133.84 -46.16 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA ASN A 93 " pdb=" C ASN A 93 " pdb=" N ARG A 94 " pdb=" CA ARG A 94 " ideal model delta harmonic sigma weight residual -180.00 -135.22 -44.78 0 5.00e+00 4.00e-02 8.02e+01 ... (remaining 7761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 2007 0.289 - 0.578: 7 0.578 - 0.867: 1 0.867 - 1.156: 2 1.156 - 1.445: 1 Chirality restraints: 2018 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.22e+01 chirality pdb=" C01 ZQU A1304 " pdb=" C02 ZQU A1304 " pdb=" C03 ZQU A1304 " pdb=" C04 ZQU A1304 " both_signs ideal model delta sigma weight residual True 1.33 2.37 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" C01 ZQU A1305 " pdb=" C02 ZQU A1305 " pdb=" C03 ZQU A1305 " pdb=" C04 ZQU A1305 " both_signs ideal model delta sigma weight residual True 1.33 2.35 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 2015 not shown) Planarity restraints: 2227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.164 2.00e-02 2.50e+03 2.82e-01 9.92e+02 pdb=" CG ASN A 98 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.497 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 7 " 0.029 2.00e-02 2.50e+03 5.84e-02 3.42e+01 pdb=" C SER B 7 " -0.101 2.00e-02 2.50e+03 pdb=" O SER B 7 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO B 8 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO B 8 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " 0.063 5.00e-02 4.00e+02 ... (remaining 2224 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 290 2.67 - 3.23: 12271 3.23 - 3.79: 19723 3.79 - 4.34: 25853 4.34 - 4.90: 43261 Nonbonded interactions: 101398 Sorted by model distance: nonbonded pdb=" O ASP A1162 " pdb=" OG1 THR A1166 " model vdw 2.115 2.440 nonbonded pdb=" OG SER A1125 " pdb=" OE1 GLU A1128 " model vdw 2.145 2.440 nonbonded pdb=" OE2 GLU A 525 " pdb=" NH1 ARG A 526 " model vdw 2.166 2.520 nonbonded pdb=" O LEU A 588 " pdb=" NH1 ARG A 592 " model vdw 2.213 2.520 nonbonded pdb=" NH1 ARG B 59 " pdb=" OD1 ASP B 65 " model vdw 2.228 2.520 ... (remaining 101393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 9.830 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.270 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.009 0.136 13014 Z= 0.604 Angle : 1.435 58.971 17645 Z= 0.675 Chirality : 0.084 1.445 2018 Planarity : 0.008 0.126 2225 Dihedral : 11.922 112.446 4738 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.36 % Favored : 93.39 % Rotamer: Outliers : 0.58 % Allowed : 6.51 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % 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: -3.97 (0.16), residues: 1621 helix: -2.87 (0.13), residues: 764 sheet: -1.63 (0.28), residues: 279 loop : -2.48 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 112 HIS 0.028 0.003 HIS A1194 PHE 0.061 0.004 PHE A 958 TYR 0.063 0.004 TYR A 952 ARG 0.017 0.002 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7629 (t160) cc_final: 0.7392 (t0) REVERT: A 94 ARG cc_start: 0.6522 (ptp90) cc_final: 0.5847 (mmm-85) REVERT: A 395 ASN cc_start: 0.7940 (t0) cc_final: 0.7706 (t0) REVERT: A 465 LEU cc_start: 0.7324 (tp) cc_final: 0.7110 (tp) REVERT: A 507 ASN cc_start: 0.7674 (t0) cc_final: 0.7407 (t0) REVERT: A 706 GLU cc_start: 0.7431 (pm20) cc_final: 0.7114 (pm20) REVERT: A 842 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5590 (mm) REVERT: A 869 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 886 LYS cc_start: 0.7175 (mttt) cc_final: 0.6847 (tptt) REVERT: A 931 MET cc_start: 0.7897 (mmp) cc_final: 0.7313 (mmm) REVERT: A 1118 GLU cc_start: 0.7633 (pp20) cc_final: 0.7102 (pm20) REVERT: A 1211 LYS cc_start: 0.7280 (pptt) cc_final: 0.6933 (pttm) REVERT: A 1218 ASP cc_start: 0.7453 (m-30) cc_final: 0.6989 (m-30) REVERT: B 153 LYS cc_start: 0.7734 (tptt) cc_final: 0.7356 (tptp) REVERT: C 67 LYS cc_start: 0.7953 (pttm) cc_final: 0.7472 (tmmt) REVERT: C 83 PHE cc_start: 0.7259 (t80) cc_final: 0.7056 (t80) REVERT: C 85 SER cc_start: 0.8280 (m) cc_final: 0.7867 (p) REVERT: C 200 GLN cc_start: 0.7894 (mt0) cc_final: 0.7613 (mt0) REVERT: C 216 ASP cc_start: 0.7644 (m-30) cc_final: 0.7429 (t70) REVERT: C 219 ILE cc_start: 0.6801 (pp) cc_final: 0.6495 (mp) outliers start: 6 outliers final: 1 residues processed: 228 average time/residue: 0.2873 time to fit residues: 91.8886 Evaluate side-chains 137 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 0.0040 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 105 ASN A 152 HIS A 269 GLN A 420 GLN A 569 GLN A 586 HIS ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 838 ASN A 935 HIS A 965 HIS A 989 GLN ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN B 18 GLN B 130 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13014 Z= 0.212 Angle : 0.808 15.565 17645 Z= 0.390 Chirality : 0.051 0.671 2018 Planarity : 0.006 0.106 2225 Dihedral : 7.432 71.987 1846 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 3.14 % Allowed : 11.84 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % 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: -2.14 (0.19), residues: 1621 helix: -0.87 (0.17), residues: 764 sheet: -1.21 (0.29), residues: 279 loop : -2.08 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 112 HIS 0.005 0.001 HIS A1194 PHE 0.018 0.002 PHE A 769 TYR 0.021 0.002 TYR C 32 ARG 0.010 0.001 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: A 90 ASN cc_start: 0.7820 (t0) cc_final: 0.7516 (t0) REVERT: A 94 ARG cc_start: 0.6543 (ptp90) cc_final: 0.6007 (mmm-85) REVERT: A 391 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6777 (tp) REVERT: A 393 PHE cc_start: 0.7210 (m-10) cc_final: 0.6998 (m-10) REVERT: A 395 ASN cc_start: 0.7974 (t0) cc_final: 0.7713 (t0) REVERT: A 414 LEU cc_start: 0.6788 (mp) cc_final: 0.6558 (tp) REVERT: A 497 ASP cc_start: 0.8005 (t0) cc_final: 0.7721 (t0) REVERT: A 507 ASN cc_start: 0.7547 (t0) cc_final: 0.7267 (t0) REVERT: A 795 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7715 (mtm) REVERT: A 869 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 877 MET cc_start: 0.7470 (tmt) cc_final: 0.6680 (tmt) REVERT: A 886 LYS cc_start: 0.7186 (mttt) cc_final: 0.6904 (tptt) REVERT: A 890 GLU cc_start: 0.7723 (pt0) cc_final: 0.6693 (tm-30) REVERT: A 909 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5829 (pp) REVERT: A 931 MET cc_start: 0.7720 (mmp) cc_final: 0.7419 (mmm) REVERT: A 968 MET cc_start: 0.7805 (mtp) cc_final: 0.7521 (ttm) REVERT: A 1118 GLU cc_start: 0.7453 (pp20) cc_final: 0.6968 (pm20) REVERT: A 1211 LYS cc_start: 0.7257 (pptt) cc_final: 0.6914 (pttm) REVERT: A 1218 ASP cc_start: 0.7078 (m-30) cc_final: 0.6875 (m-30) REVERT: A 1251 LYS cc_start: 0.6143 (tptp) cc_final: 0.5711 (ttmt) REVERT: B 24 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7427 (mtp85) REVERT: B 51 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 67 LYS cc_start: 0.8027 (pttm) cc_final: 0.7512 (tmmt) REVERT: C 85 SER cc_start: 0.8177 (m) cc_final: 0.7714 (p) REVERT: C 200 GLN cc_start: 0.7942 (mt0) cc_final: 0.7735 (mt0) REVERT: C 216 ASP cc_start: 0.7804 (m-30) cc_final: 0.7587 (t70) outliers start: 41 outliers final: 19 residues processed: 194 average time/residue: 0.2531 time to fit residues: 71.9503 Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 537 ARG Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN C 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.004 0.036 13014 Z= 0.233 Angle : 0.780 15.697 17645 Z= 0.374 Chirality : 0.051 0.649 2018 Planarity : 0.005 0.101 2225 Dihedral : 6.914 69.596 1846 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 4.02 % Allowed : 12.35 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % 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: 1621 helix: -0.22 (0.18), residues: 775 sheet: -0.93 (0.30), residues: 279 loop : -1.83 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 112 HIS 0.004 0.001 HIS A 935 PHE 0.033 0.002 PHE A 769 TYR 0.018 0.002 TYR A1132 ARG 0.008 0.001 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7728 (t0) cc_final: 0.7513 (t0) REVERT: A 110 MET cc_start: 0.7128 (mmm) cc_final: 0.6902 (tpp) REVERT: A 395 ASN cc_start: 0.8063 (t0) cc_final: 0.7792 (t0) REVERT: A 507 ASN cc_start: 0.7585 (t0) cc_final: 0.7292 (t0) REVERT: A 795 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7713 (mtm) REVERT: A 886 LYS cc_start: 0.7176 (mttt) cc_final: 0.6915 (tptt) REVERT: A 890 GLU cc_start: 0.7689 (pt0) cc_final: 0.6713 (tm-30) REVERT: A 909 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5855 (pp) REVERT: A 968 MET cc_start: 0.7782 (mtp) cc_final: 0.6832 (ttm) REVERT: A 1008 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 1211 LYS cc_start: 0.7284 (pptt) cc_final: 0.6936 (pttm) REVERT: A 1218 ASP cc_start: 0.7056 (m-30) cc_final: 0.6840 (m-30) REVERT: B 24 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7586 (mtp85) REVERT: B 172 GLN cc_start: 0.6186 (tp-100) cc_final: 0.5980 (tp40) REVERT: C 67 LYS cc_start: 0.8025 (pttm) cc_final: 0.7388 (tmmt) REVERT: C 85 SER cc_start: 0.8072 (m) cc_final: 0.7587 (p) REVERT: C 89 GLU cc_start: 0.7993 (mp0) cc_final: 0.7736 (pm20) outliers start: 54 outliers final: 30 residues processed: 178 average time/residue: 0.2389 time to fit residues: 62.1525 Evaluate side-chains 160 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 537 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13014 Z= 0.208 Angle : 0.758 15.190 17645 Z= 0.359 Chirality : 0.050 0.614 2018 Planarity : 0.005 0.098 2225 Dihedral : 6.532 67.150 1844 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 3.73 % Allowed : 13.67 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1621 helix: 0.18 (0.19), residues: 775 sheet: -0.65 (0.31), residues: 284 loop : -1.58 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 102 HIS 0.003 0.001 HIS A 935 PHE 0.030 0.002 PHE A 769 TYR 0.018 0.002 TYR A1132 ARG 0.005 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7282 (mmm) cc_final: 0.6912 (tpt) REVERT: A 395 ASN cc_start: 0.8010 (t0) cc_final: 0.7755 (t0) REVERT: A 439 MET cc_start: 0.8598 (tpp) cc_final: 0.8330 (tpp) REVERT: A 497 ASP cc_start: 0.8051 (t0) cc_final: 0.7753 (t0) REVERT: A 507 ASN cc_start: 0.7607 (t0) cc_final: 0.7293 (t0) REVERT: A 742 ASP cc_start: 0.7373 (m-30) cc_final: 0.7028 (m-30) REVERT: A 769 PHE cc_start: 0.7178 (p90) cc_final: 0.6869 (p90) REVERT: A 790 MET cc_start: 0.7204 (mtm) cc_final: 0.6953 (mtm) REVERT: A 883 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 886 LYS cc_start: 0.7167 (mttt) cc_final: 0.6910 (tptt) REVERT: A 890 GLU cc_start: 0.7629 (pt0) cc_final: 0.6509 (tm-30) REVERT: A 992 SER cc_start: 0.7721 (t) cc_final: 0.7484 (p) REVERT: A 1008 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 1118 GLU cc_start: 0.7371 (pm20) cc_final: 0.7007 (pm20) REVERT: A 1218 ASP cc_start: 0.7065 (m-30) cc_final: 0.6850 (m-30) REVERT: B 37 TYR cc_start: 0.7778 (m-80) cc_final: 0.6369 (m-80) REVERT: B 130 GLN cc_start: 0.6512 (tt0) cc_final: 0.6312 (tt0) REVERT: C 67 LYS cc_start: 0.7987 (pttm) cc_final: 0.7299 (tmmt) REVERT: C 85 SER cc_start: 0.7906 (m) cc_final: 0.7390 (p) REVERT: C 89 GLU cc_start: 0.7966 (mp0) cc_final: 0.7730 (pm20) REVERT: C 157 GLU cc_start: 0.7033 (pt0) cc_final: 0.6787 (tp30) REVERT: C 200 GLN cc_start: 0.7713 (mt0) cc_final: 0.7486 (mt0) outliers start: 50 outliers final: 32 residues processed: 183 average time/residue: 0.2414 time to fit residues: 65.0321 Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 420 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13014 Z= 0.197 Angle : 0.740 15.027 17645 Z= 0.351 Chirality : 0.049 0.621 2018 Planarity : 0.004 0.096 2225 Dihedral : 6.412 67.865 1844 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 3.65 % Allowed : 14.04 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1621 helix: 0.44 (0.19), residues: 772 sheet: -0.49 (0.32), residues: 280 loop : -1.54 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 102 HIS 0.003 0.001 HIS A 517 PHE 0.031 0.001 PHE A 769 TYR 0.018 0.001 TYR A1132 ARG 0.004 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 122 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6322 (ptp90) cc_final: 0.6070 (mmm-85) REVERT: A 110 MET cc_start: 0.7327 (mmm) cc_final: 0.6936 (tpt) REVERT: A 309 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6523 (t80) REVERT: A 352 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: A 395 ASN cc_start: 0.8011 (t0) cc_final: 0.7745 (t0) REVERT: A 507 ASN cc_start: 0.7611 (t0) cc_final: 0.7338 (t0) REVERT: A 626 MET cc_start: 0.5757 (mmm) cc_final: 0.5429 (mtm) REVERT: A 742 ASP cc_start: 0.7421 (m-30) cc_final: 0.7148 (m-30) REVERT: A 769 PHE cc_start: 0.7115 (p90) cc_final: 0.6893 (p90) REVERT: A 795 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: A 883 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 886 LYS cc_start: 0.7151 (mttt) cc_final: 0.6890 (tptt) REVERT: A 890 GLU cc_start: 0.7593 (pt0) cc_final: 0.6554 (tm-30) REVERT: A 992 SER cc_start: 0.7661 (t) cc_final: 0.7442 (p) REVERT: B 102 TRP cc_start: 0.9326 (OUTLIER) cc_final: 0.8113 (m100) REVERT: C 67 LYS cc_start: 0.7884 (pttm) cc_final: 0.7045 (ttpt) REVERT: C 85 SER cc_start: 0.7824 (m) cc_final: 0.7329 (p) outliers start: 49 outliers final: 29 residues processed: 163 average time/residue: 0.2327 time to fit residues: 56.9738 Evaluate side-chains 146 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13014 Z= 0.238 Angle : 0.756 15.281 17645 Z= 0.361 Chirality : 0.050 0.629 2018 Planarity : 0.005 0.095 2225 Dihedral : 6.394 67.840 1844 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 3.58 % Allowed : 14.33 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1621 helix: 0.50 (0.19), residues: 765 sheet: -0.44 (0.32), residues: 280 loop : -1.50 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 102 HIS 0.003 0.001 HIS A 965 PHE 0.031 0.002 PHE A 769 TYR 0.019 0.002 TYR A1132 ARG 0.003 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 113 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7334 (mmm) cc_final: 0.6936 (tpt) REVERT: A 352 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: A 395 ASN cc_start: 0.7962 (t0) cc_final: 0.7657 (t0) REVERT: A 449 MET cc_start: 0.6222 (ttp) cc_final: 0.5939 (tmm) REVERT: A 507 ASN cc_start: 0.7635 (t0) cc_final: 0.7352 (t0) REVERT: A 769 PHE cc_start: 0.7157 (p90) cc_final: 0.6888 (p90) REVERT: A 869 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6900 (mp) REVERT: A 883 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (mm) REVERT: A 886 LYS cc_start: 0.7187 (mttt) cc_final: 0.6933 (tptt) REVERT: A 890 GLU cc_start: 0.7561 (pt0) cc_final: 0.6547 (tm-30) REVERT: A 989 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 992 SER cc_start: 0.7725 (t) cc_final: 0.7496 (p) REVERT: B 102 TRP cc_start: 0.9367 (OUTLIER) cc_final: 0.8164 (m100) REVERT: C 67 LYS cc_start: 0.7916 (pttm) cc_final: 0.7115 (ttpt) REVERT: C 85 SER cc_start: 0.7880 (m) cc_final: 0.7383 (p) outliers start: 48 outliers final: 34 residues processed: 150 average time/residue: 0.2426 time to fit residues: 55.0092 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN C 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13014 Z= 0.205 Angle : 0.736 15.071 17645 Z= 0.349 Chirality : 0.049 0.612 2018 Planarity : 0.004 0.094 2225 Dihedral : 6.267 66.841 1844 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 3.58 % Allowed : 14.69 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1621 helix: 0.61 (0.19), residues: 765 sheet: -0.37 (0.32), residues: 287 loop : -1.43 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 102 HIS 0.003 0.001 HIS A 935 PHE 0.031 0.001 PHE A 769 TYR 0.019 0.002 TYR A1132 ARG 0.003 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 122 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7277 (mmm) cc_final: 0.6854 (tpt) REVERT: A 309 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 352 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: A 395 ASN cc_start: 0.7922 (t0) cc_final: 0.7618 (t0) REVERT: A 449 MET cc_start: 0.6264 (ttp) cc_final: 0.5917 (tmm) REVERT: A 496 MET cc_start: 0.6145 (tpp) cc_final: 0.5912 (tpp) REVERT: A 507 ASN cc_start: 0.7649 (t0) cc_final: 0.7360 (t0) REVERT: A 511 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6653 (p90) REVERT: A 769 PHE cc_start: 0.7112 (p90) cc_final: 0.6797 (p90) REVERT: A 790 MET cc_start: 0.7064 (mtm) cc_final: 0.6779 (mtm) REVERT: A 869 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6901 (mp) REVERT: A 877 MET cc_start: 0.7551 (tmt) cc_final: 0.6694 (tmt) REVERT: A 883 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 886 LYS cc_start: 0.7156 (mttt) cc_final: 0.6919 (tptt) REVERT: A 890 GLU cc_start: 0.7559 (pt0) cc_final: 0.6521 (tm-30) REVERT: A 992 SER cc_start: 0.7676 (t) cc_final: 0.7469 (p) REVERT: A 1269 MET cc_start: -0.2008 (mtm) cc_final: -0.3461 (ppp) REVERT: B 24 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7176 (mtt90) REVERT: B 102 TRP cc_start: 0.9341 (OUTLIER) cc_final: 0.8123 (m100) REVERT: C 67 LYS cc_start: 0.7911 (pttm) cc_final: 0.7090 (ttpt) REVERT: C 85 SER cc_start: 0.7889 (m) cc_final: 0.7434 (p) outliers start: 48 outliers final: 38 residues processed: 161 average time/residue: 0.2342 time to fit residues: 57.1258 Evaluate side-chains 154 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 0.0030 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13014 Z= 0.168 Angle : 0.719 14.959 17645 Z= 0.339 Chirality : 0.048 0.602 2018 Planarity : 0.004 0.093 2225 Dihedral : 6.146 66.041 1844 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 3.65 % Allowed : 14.62 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1621 helix: 0.84 (0.19), residues: 760 sheet: -0.25 (0.32), residues: 287 loop : -1.36 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.002 0.001 HIS A 517 PHE 0.031 0.001 PHE A 769 TYR 0.018 0.001 TYR A1132 ARG 0.003 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 122 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6370 (ptp90) cc_final: 0.6110 (mmm-85) REVERT: A 110 MET cc_start: 0.7252 (mmm) cc_final: 0.6845 (tpt) REVERT: A 309 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6669 (t80) REVERT: A 352 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: A 395 ASN cc_start: 0.7894 (t0) cc_final: 0.7609 (t0) REVERT: A 439 MET cc_start: 0.8544 (tpp) cc_final: 0.8227 (tpp) REVERT: A 449 MET cc_start: 0.6251 (ttp) cc_final: 0.5876 (tmm) REVERT: A 507 ASN cc_start: 0.7632 (t0) cc_final: 0.7352 (t0) REVERT: A 511 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6686 (p90) REVERT: A 790 MET cc_start: 0.7077 (mtm) cc_final: 0.6875 (mtm) REVERT: A 869 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6901 (mp) REVERT: A 877 MET cc_start: 0.7531 (tmt) cc_final: 0.6737 (tmt) REVERT: A 883 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 886 LYS cc_start: 0.7108 (mttt) cc_final: 0.6898 (tptt) REVERT: A 890 GLU cc_start: 0.7587 (pt0) cc_final: 0.6599 (tm-30) REVERT: A 1008 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 1118 GLU cc_start: 0.7184 (pm20) cc_final: 0.6812 (pm20) REVERT: A 1251 LYS cc_start: 0.5679 (tptp) cc_final: 0.5230 (pttt) REVERT: B 24 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7188 (mtt90) REVERT: B 102 TRP cc_start: 0.9284 (OUTLIER) cc_final: 0.8105 (m100) REVERT: B 191 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6593 (mm-30) REVERT: C 67 LYS cc_start: 0.7937 (pttm) cc_final: 0.7058 (ttpt) outliers start: 49 outliers final: 34 residues processed: 161 average time/residue: 0.2383 time to fit residues: 57.7082 Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 114 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13014 Z= 0.178 Angle : 0.725 15.045 17645 Z= 0.344 Chirality : 0.049 0.606 2018 Planarity : 0.004 0.091 2225 Dihedral : 6.107 66.330 1844 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.51 % Allowed : 15.35 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1621 helix: 0.85 (0.19), residues: 767 sheet: -0.04 (0.33), residues: 275 loop : -1.37 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 102 HIS 0.002 0.001 HIS B 98 PHE 0.027 0.001 PHE A 769 TYR 0.019 0.001 TYR A1132 ARG 0.005 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 111 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7187 (mmm) cc_final: 0.6751 (tpt) REVERT: A 309 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 352 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: A 392 GLU cc_start: 0.7220 (tt0) cc_final: 0.6350 (tm-30) REVERT: A 395 ASN cc_start: 0.7762 (t0) cc_final: 0.7553 (t0) REVERT: A 449 MET cc_start: 0.6274 (ttp) cc_final: 0.5163 (tmm) REVERT: A 496 MET cc_start: 0.5987 (tpp) cc_final: 0.5707 (tpp) REVERT: A 507 ASN cc_start: 0.7580 (t0) cc_final: 0.7303 (t0) REVERT: A 511 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 790 MET cc_start: 0.7109 (mtm) cc_final: 0.6908 (mtm) REVERT: A 869 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6927 (mp) REVERT: A 877 MET cc_start: 0.7490 (tmt) cc_final: 0.6649 (tmt) REVERT: A 883 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7755 (mm) REVERT: A 886 LYS cc_start: 0.7103 (mttt) cc_final: 0.6868 (tptt) REVERT: A 989 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: A 1008 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 1118 GLU cc_start: 0.7189 (pm20) cc_final: 0.6808 (pm20) REVERT: A 1251 LYS cc_start: 0.5724 (tptp) cc_final: 0.5249 (pttt) REVERT: B 24 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7325 (mtp85) REVERT: B 102 TRP cc_start: 0.9313 (OUTLIER) cc_final: 0.8116 (m100) REVERT: C 67 LYS cc_start: 0.7892 (pttm) cc_final: 0.7026 (ttpt) outliers start: 47 outliers final: 36 residues processed: 147 average time/residue: 0.2342 time to fit residues: 51.9566 Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 161 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13014 Z= 0.161 Angle : 0.713 14.912 17645 Z= 0.338 Chirality : 0.048 0.596 2018 Planarity : 0.004 0.091 2225 Dihedral : 6.008 65.746 1844 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.36 % Allowed : 15.79 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1621 helix: 1.01 (0.19), residues: 761 sheet: -0.06 (0.32), residues: 282 loop : -1.33 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.002 0.000 HIS B 39 PHE 0.029 0.001 PHE A 769 TYR 0.019 0.001 TYR A1132 ARG 0.003 0.000 ARG B 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8349 (t70) cc_final: 0.8103 (t70) REVERT: A 110 MET cc_start: 0.7181 (mmm) cc_final: 0.6755 (tpt) REVERT: A 309 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 352 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: A 392 GLU cc_start: 0.7226 (tt0) cc_final: 0.6386 (tm-30) REVERT: A 395 ASN cc_start: 0.7719 (t0) cc_final: 0.7484 (t0) REVERT: A 439 MET cc_start: 0.8434 (tpp) cc_final: 0.8206 (tpp) REVERT: A 449 MET cc_start: 0.6265 (ttp) cc_final: 0.5110 (tmm) REVERT: A 507 ASN cc_start: 0.7576 (t0) cc_final: 0.7309 (t0) REVERT: A 511 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6715 (p90) REVERT: A 790 MET cc_start: 0.7090 (mtm) cc_final: 0.6784 (mtm) REVERT: A 799 ASP cc_start: 0.7690 (p0) cc_final: 0.7445 (p0) REVERT: A 883 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 904 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.7072 (tpp80) REVERT: A 952 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6440 (t80) REVERT: A 989 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: A 1008 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 1118 GLU cc_start: 0.7159 (pm20) cc_final: 0.6780 (pm20) REVERT: A 1232 ARG cc_start: 0.5556 (ttm-80) cc_final: 0.5238 (ptm160) REVERT: A 1251 LYS cc_start: 0.5756 (tptp) cc_final: 0.5274 (pttt) REVERT: B 24 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7368 (mtp85) REVERT: B 161 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.7075 (ttp-110) REVERT: C 67 LYS cc_start: 0.7822 (pttm) cc_final: 0.7009 (ttpt) outliers start: 45 outliers final: 30 residues processed: 153 average time/residue: 0.2396 time to fit residues: 54.9385 Evaluate side-chains 142 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121299 restraints weight = 38826.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124631 restraints weight = 48252.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126347 restraints weight = 16540.408| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13014 Z= 0.199 Angle : 0.740 15.089 17645 Z= 0.351 Chirality : 0.049 0.608 2018 Planarity : 0.004 0.092 2225 Dihedral : 6.045 66.546 1844 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 3.22 % Allowed : 16.30 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1621 helix: 0.98 (0.19), residues: 758 sheet: -0.08 (0.32), residues: 277 loop : -1.26 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 102 HIS 0.003 0.001 HIS B 39 PHE 0.028 0.001 PHE A 769 TYR 0.019 0.001 TYR A1132 ARG 0.003 0.000 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.66 seconds wall clock time: 46 minutes 50.00 seconds (2810.00 seconds total)