Starting phenix.real_space_refine on Sat Sep 12 00:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704.map" model { file = "/net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kl9_0704/09_2026/6kl9_0704_neut.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 39 5.16 5 C 7722 2.51 5 N 2005 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1180, 9711 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 1155} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 1180, 9711 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 1155} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 9895 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS A 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 775 " occ=0.50 Time building chain proxies: 4.28, per 1000 atoms: 0.35 Number of scatterers: 12191 At special positions: 0 Unit cell: (124.2, 125.28, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 25 15.00 Mg 2 11.99 O 2398 8.00 N 2005 7.00 C 7722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS C 131 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 809.6 milliseconds 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 46.3% alpha, 10.5% beta 4 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.700A pdb=" N LYS A 6 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.762A pdb=" N VAL A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.539A pdb=" N TYR A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 4.446A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.680A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 178 through 194 removed outlier: 4.108A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.508A pdb=" N LYS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.679A pdb=" N GLU A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.895A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.422A pdb=" N ASN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.641A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.890A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.921A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.643A pdb=" N GLU A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 409 through 432 Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.615A pdb=" N VAL A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.109A pdb=" N LEU A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.831A pdb=" N GLN A 567 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 591 removed outlier: 4.342A pdb=" N LYS A 591 " --> pdb=" O GLY A 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 591' Processing helix chain 'A' and resid 592 through 598 removed outlier: 4.034A pdb=" N VAL A 596 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.052A pdb=" N VAL A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.699A pdb=" N MET A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.874A pdb=" N LEU A 756 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.648A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 790 " --> pdb=" O LYS A 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 786 through 790' Processing helix chain 'A' and resid 811 through 822 removed outlier: 3.573A pdb=" N GLU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.795A pdb=" N GLU A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.852A pdb=" N GLU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1101 through 1104 removed outlier: 4.180A pdb=" N ILE A1104 " --> pdb=" O LYS A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1104' Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.478A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.612A pdb=" N ASN A1182 " --> pdb=" O ASN A1178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 removed outlier: 3.646A pdb=" N VAL A1209 " --> pdb=" O LEU A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 118 through 149 removed outlier: 3.869A pdb=" N LEU B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.506A pdb=" N LEU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.026A pdb=" N LEU C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.754A pdb=" N LEU C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.827A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 204 " --> pdb=" O THR C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.586A pdb=" N LEU C 232 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.688A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 20 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 546 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.688A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.814A pdb=" N PHE A 244 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 252 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA5, first strand: chain 'A' and resid 758 through 759 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 855 Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.627A pdb=" N ALA A1046 " --> pdb=" O ARG A1033 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB2, first strand: chain 'A' and resid 1138 through 1140 Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.788A pdb=" N GLU B 180 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 183 through 187 removed outlier: 4.917A pdb=" N CYS B 185 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N CYS B 195 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.502A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3559 1.34 - 1.46: 3047 1.46 - 1.58: 5760 1.58 - 1.71: 48 1.71 - 1.83: 63 Bond restraints: 12477 Sorted by residual: bond pdb=" C LEU A 128 " pdb=" N PRO A 129 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.20e-02 6.94e+03 5.14e+00 bond pdb=" N9 A G 17 " pdb=" C4 A G 17 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 3.89e+00 bond pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.27e-02 6.20e+03 3.71e+00 bond pdb=" N ARG B 187 " pdb=" CA ARG B 187 " ideal model delta sigma weight residual 1.454 1.476 -0.021 1.15e-02 7.56e+03 3.48e+00 bond pdb=" O3' U G 7 " pdb=" P A G 8 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.20e-02 6.94e+03 3.46e+00 ... (remaining 12472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 16525 2.84 - 5.69: 323 5.69 - 8.53: 52 8.53 - 11.37: 12 11.37 - 14.22: 1 Bond angle restraints: 16913 Sorted by residual: angle pdb=" N PHE A 131 " pdb=" CA PHE A 131 " pdb=" C PHE A 131 " ideal model delta sigma weight residual 111.03 121.19 -10.16 1.11e+00 8.12e-01 8.38e+01 angle pdb=" N ASP A 450 " pdb=" CA ASP A 450 " pdb=" C ASP A 450 " ideal model delta sigma weight residual 111.28 120.45 -9.17 1.09e+00 8.42e-01 7.07e+01 angle pdb=" N LEU A1047 " pdb=" CA LEU A1047 " pdb=" C LEU A1047 " ideal model delta sigma weight residual 108.48 122.70 -14.22 1.80e+00 3.09e-01 6.24e+01 angle pdb=" N VAL A 758 " pdb=" CA VAL A 758 " pdb=" C VAL A 758 " ideal model delta sigma weight residual 108.27 118.12 -9.85 1.37e+00 5.33e-01 5.17e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 114.75 106.59 8.16 1.26e+00 6.30e-01 4.20e+01 ... (remaining 16908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7475 35.95 - 71.90: 125 71.90 - 107.86: 9 107.86 - 143.81: 2 143.81 - 179.76: 3 Dihedral angle restraints: 7614 sinusoidal: 3412 harmonic: 4202 Sorted by residual: dihedral pdb=" O4' C G 21 " pdb=" C1' C G 21 " pdb=" N1 C G 21 " pdb=" C2 C G 21 " ideal model delta sinusoidal sigma weight residual -128.00 51.76 -179.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -128.00 50.39 -178.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual -86.00 -141.09 55.09 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 7611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1676 0.099 - 0.198: 143 0.198 - 0.298: 20 0.298 - 0.397: 4 0.397 - 0.496: 2 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA ASN A 928 " pdb=" N ASN A 928 " pdb=" C ASN A 928 " pdb=" CB ASN A 928 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CA LEU A1047 " pdb=" N LEU A1047 " pdb=" C LEU A1047 " pdb=" CB LEU A1047 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 1842 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 991 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLY A 991 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 991 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 992 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 720 " 0.021 2.00e-02 2.50e+03 2.58e-02 9.98e+00 pdb=" CG HIS A 720 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 720 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 720 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 720 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 720 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 527 " -0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 528 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 528 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 528 " -0.042 5.00e-02 4.00e+02 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 96 2.60 - 3.18: 9696 3.18 - 3.75: 17176 3.75 - 4.33: 24374 4.33 - 4.90: 39653 Nonbonded interactions: 90995 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.031 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 205 " model vdw 2.035 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.036 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 206 " model vdw 2.045 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.046 2.170 ... (remaining 90990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12478 Z= 0.260 Angle : 1.015 14.216 16915 Z= 0.634 Chirality : 0.063 0.496 1845 Planarity : 0.007 0.077 2077 Dihedral : 13.562 179.759 4899 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.74 % Favored : 90.04 % Rotamer: Outliers : 2.72 % Allowed : 2.95 % Favored : 94.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.16), residues: 1399 helix: -3.28 (0.13), residues: 585 sheet: -0.77 (0.57), residues: 87 loop : -3.52 (0.18), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 543 TYR 0.027 0.002 TYR A1049 PHE 0.027 0.002 PHE A 474 TRP 0.035 0.003 TRP A1218 HIS 0.031 0.002 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.26 (12477) covalent geometry : angle 1.01513 / 0.63 (16913) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 2.44960 / 1.41 ( 2) hydrogen bonds : bond 0.16885 / 11.01 ( 496) hydrogen bonds : angle 9.14442 / 6.07 ( 1379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7748 (t70) cc_final: 0.7458 (t-90) REVERT: A 107 LYS cc_start: 0.8050 (tptm) cc_final: 0.7435 (tttm) REVERT: A 135 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7582 (mmtt) REVERT: A 179 ASN cc_start: 0.7659 (m-40) cc_final: 0.7435 (m-40) REVERT: A 278 LYS cc_start: 0.7699 (mppt) cc_final: 0.7006 (pttp) REVERT: A 875 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 878 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7478 (tttt) REVERT: A 925 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: A 1003 LYS cc_start: 0.8200 (mtmp) cc_final: 0.7872 (mtpt) REVERT: A 1112 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.5035 (ttp-170) REVERT: A 1133 LEU cc_start: 0.8255 (mp) cc_final: 0.7973 (tp) REVERT: A 1137 MET cc_start: 0.7040 (ttm) cc_final: 0.6830 (mtp) REVERT: A 1204 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 132 ILE cc_start: 0.8202 (mt) cc_final: 0.7995 (mt) REVERT: B 134 LYS cc_start: 0.7596 (mttm) cc_final: 0.6960 (mttt) REVERT: B 158 VAL cc_start: 0.8604 (t) cc_final: 0.8127 (m) REVERT: B 166 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6828 (p0) REVERT: B 169 ASN cc_start: 0.7894 (t0) cc_final: 0.7569 (t0) REVERT: B 188 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 209 TYR cc_start: 0.8462 (m-80) cc_final: 0.8129 (m-10) REVERT: B 217 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7515 (ptt-90) REVERT: B 222 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7149 (mtm-85) outliers start: 34 outliers final: 22 residues processed: 371 average time/residue: 0.1238 time to fit residues: 64.2448 Evaluate side-chains 226 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 222 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 268 GLN A 306 ASN A 577 ASN A 582 ASN A 803 ASN A 813 ASN A 955 ASN A 963 ASN A1012 ASN A1051 ASN C 145 ASN C 231 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.207259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175690 restraints weight = 30493.579| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 4.20 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12478 Z= 0.162 Angle : 0.691 10.429 16915 Z= 0.380 Chirality : 0.046 0.287 1845 Planarity : 0.005 0.069 2077 Dihedral : 15.342 176.679 1991 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.74 % Favored : 91.12 % Rotamer: Outliers : 2.41 % Allowed : 11.34 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.19), residues: 1399 helix: -1.25 (0.18), residues: 589 sheet: -1.18 (0.55), residues: 95 loop : -3.10 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 217 TYR 0.023 0.002 TYR A1036 PHE 0.028 0.002 PHE A 173 TRP 0.019 0.002 TRP A1218 HIS 0.014 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (12477) covalent geometry : angle 0.68508 / 0.38 (16913) SS BOND : bond 0.01674 / 0.88 ( 1) SS BOND : angle 8.02146 / 4.30 ( 2) hydrogen bonds : bond 0.06604 / 4.52 ( 496) hydrogen bonds : angle 6.28301 / 4.05 ( 1379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8251 (tptm) cc_final: 0.7893 (ttpt) REVERT: A 135 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7069 (mmmt) REVERT: A 138 ILE cc_start: 0.8351 (tt) cc_final: 0.8144 (mm) REVERT: A 268 GLN cc_start: 0.5505 (mm-40) cc_final: 0.4961 (mt0) REVERT: A 471 LYS cc_start: 0.7605 (tmmt) cc_final: 0.7212 (tttt) REVERT: A 765 ILE cc_start: 0.6727 (pt) cc_final: 0.6339 (tp) REVERT: A 875 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 1003 LYS cc_start: 0.8291 (mtmp) cc_final: 0.8023 (mtpt) REVERT: A 1033 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6858 (ttt-90) REVERT: A 1112 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5599 (ttp-170) REVERT: A 1133 LEU cc_start: 0.8342 (mp) cc_final: 0.8069 (tt) REVERT: A 1137 MET cc_start: 0.7208 (ttm) cc_final: 0.6988 (mtp) REVERT: B 169 ASN cc_start: 0.7077 (t0) cc_final: 0.6833 (t0) REVERT: B 188 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7887 (t80) REVERT: C 135 GLU cc_start: 0.5537 (mm-30) cc_final: 0.5237 (mm-30) outliers start: 30 outliers final: 12 residues processed: 238 average time/residue: 0.1085 time to fit residues: 37.8352 Evaluate side-chains 200 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 192 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 142 ASN A 340 ASN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS A 989 GLN A1051 ASN C 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.200218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167142 restraints weight = 33206.657| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.40 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 12478 Z= 0.260 Angle : 0.745 10.332 16915 Z= 0.406 Chirality : 0.050 0.233 1845 Planarity : 0.005 0.057 2077 Dihedral : 14.497 174.634 1951 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.81 % Favored : 90.04 % Rotamer: Outliers : 3.81 % Allowed : 11.58 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.20), residues: 1399 helix: -0.46 (0.20), residues: 594 sheet: -1.21 (0.52), residues: 103 loop : -3.05 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 155 TYR 0.027 0.002 TYR A1185 PHE 0.056 0.003 PHE A1027 TRP 0.016 0.002 TRP A1218 HIS 0.033 0.003 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (12477) covalent geometry : angle 0.74071 / 0.40 (16913) SS BOND : bond 0.01286 / 0.68 ( 1) SS BOND : angle 7.17260 / 3.78 ( 2) hydrogen bonds : bond 0.07646 / 5.21 ( 496) hydrogen bonds : angle 5.91678 / 3.83 ( 1379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8050 (tptm) cc_final: 0.7693 (tttt) REVERT: A 135 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7241 (mmmt) REVERT: A 189 ILE cc_start: 0.7813 (mt) cc_final: 0.7602 (mt) REVERT: A 268 GLN cc_start: 0.5660 (mm-40) cc_final: 0.5031 (mm-40) REVERT: A 875 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 1133 LEU cc_start: 0.8489 (mp) cc_final: 0.7997 (tt) REVERT: A 1137 MET cc_start: 0.7302 (ttm) cc_final: 0.7041 (mtp) REVERT: B 134 LYS cc_start: 0.7310 (mttt) cc_final: 0.7000 (mttt) REVERT: B 188 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8235 (t80) REVERT: C 196 PHE cc_start: 0.6499 (m-10) cc_final: 0.6220 (m-10) outliers start: 48 outliers final: 34 residues processed: 227 average time/residue: 0.0981 time to fit residues: 33.8854 Evaluate side-chains 216 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 26 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 793 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170165 restraints weight = 28861.695| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 4.13 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12478 Z= 0.153 Angle : 0.640 9.536 16915 Z= 0.352 Chirality : 0.045 0.205 1845 Planarity : 0.004 0.052 2077 Dihedral : 14.239 177.142 1941 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.74 % Favored : 91.12 % Rotamer: Outliers : 3.19 % Allowed : 12.59 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.21), residues: 1399 helix: 0.16 (0.21), residues: 589 sheet: -1.14 (0.52), residues: 105 loop : -2.87 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 187 TYR 0.027 0.002 TYR C 197 PHE 0.036 0.002 PHE A1027 TRP 0.011 0.002 TRP A1193 HIS 0.012 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12477) covalent geometry : angle 0.63645 / 0.35 (16913) SS BOND : bond 0.00867 / 0.46 ( 1) SS BOND : angle 5.89245 / 3.10 ( 2) hydrogen bonds : bond 0.06266 / 4.32 ( 496) hydrogen bonds : angle 5.47839 / 3.52 ( 1379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8173 (tptm) cc_final: 0.7851 (tttt) REVERT: A 189 ILE cc_start: 0.7755 (mt) cc_final: 0.7544 (mt) REVERT: A 268 GLN cc_start: 0.5608 (mm-40) cc_final: 0.5127 (mt0) REVERT: A 426 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.4753 (t80) REVERT: A 471 LYS cc_start: 0.7812 (tmmt) cc_final: 0.7534 (tttp) REVERT: A 824 ASP cc_start: 0.8187 (p0) cc_final: 0.7971 (p0) REVERT: A 875 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 1133 LEU cc_start: 0.8385 (mp) cc_final: 0.7927 (tt) REVERT: A 1137 MET cc_start: 0.7340 (ttm) cc_final: 0.7046 (mtp) REVERT: B 188 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8328 (t80) REVERT: C 135 GLU cc_start: 0.5573 (mm-30) cc_final: 0.5143 (mm-30) REVERT: C 186 MET cc_start: 0.6635 (pmm) cc_final: 0.6259 (pmm) REVERT: C 194 PRO cc_start: 0.7286 (Cg_exo) cc_final: 0.7044 (Cg_endo) REVERT: C 196 PHE cc_start: 0.6529 (m-80) cc_final: 0.6279 (m-10) outliers start: 40 outliers final: 23 residues processed: 215 average time/residue: 0.0934 time to fit residues: 30.3985 Evaluate side-chains 198 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** 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 = 0.4336 r_free = 0.4336 target = 0.206124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172104 restraints weight = 23551.772| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.87 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12478 Z= 0.130 Angle : 0.596 8.899 16915 Z= 0.329 Chirality : 0.043 0.202 1845 Planarity : 0.004 0.047 2077 Dihedral : 14.054 178.184 1932 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.74 % Favored : 91.12 % Rotamer: Outliers : 2.64 % Allowed : 13.75 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.22), residues: 1399 helix: 0.55 (0.22), residues: 588 sheet: -1.50 (0.43), residues: 141 loop : -2.79 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.014 0.001 TYR A 494 PHE 0.030 0.001 PHE A 173 TRP 0.011 0.001 TRP A1086 HIS 0.008 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (12477) covalent geometry : angle 0.59299 / 0.33 (16913) SS BOND : bond 0.00842 / 0.44 ( 1) SS BOND : angle 5.47089 / 2.88 ( 2) hydrogen bonds : bond 0.05508 / 3.83 ( 496) hydrogen bonds : angle 5.21868 / 3.35 ( 1379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7568 (mt) REVERT: A 107 LYS cc_start: 0.8208 (tptm) cc_final: 0.7899 (ttpt) REVERT: A 189 ILE cc_start: 0.7732 (mt) cc_final: 0.7528 (mt) REVERT: A 268 GLN cc_start: 0.5574 (mm-40) cc_final: 0.5036 (mt0) REVERT: A 426 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.4495 (t80) REVERT: A 471 LYS cc_start: 0.7808 (tmmt) cc_final: 0.7544 (tttp) REVERT: A 765 ILE cc_start: 0.6824 (pt) cc_final: 0.6178 (tp) REVERT: A 824 ASP cc_start: 0.8119 (p0) cc_final: 0.7905 (p0) REVERT: A 875 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 1133 LEU cc_start: 0.8284 (mp) cc_final: 0.7844 (tt) REVERT: A 1137 MET cc_start: 0.7354 (ttm) cc_final: 0.6999 (mtp) REVERT: B 134 LYS cc_start: 0.7508 (mttp) cc_final: 0.7188 (mttp) REVERT: C 184 GLU cc_start: 0.5883 (tm-30) cc_final: 0.5505 (tm-30) outliers start: 33 outliers final: 21 residues processed: 206 average time/residue: 0.1002 time to fit residues: 31.3664 Evaluate side-chains 200 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.204504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170243 restraints weight = 29972.973| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 4.26 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12478 Z= 0.140 Angle : 0.609 8.783 16915 Z= 0.333 Chirality : 0.043 0.201 1845 Planarity : 0.004 0.049 2077 Dihedral : 13.969 177.417 1930 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.33 % Rotamer: Outliers : 2.56 % Allowed : 14.14 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.22), residues: 1399 helix: 0.74 (0.22), residues: 588 sheet: -1.46 (0.42), residues: 147 loop : -2.74 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 155 TYR 0.025 0.001 TYR C 197 PHE 0.031 0.002 PHE A 173 TRP 0.008 0.001 TRP A1218 HIS 0.012 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12477) covalent geometry : angle 0.60612 / 0.33 (16913) SS BOND : bond 0.00815 / 0.43 ( 1) SS BOND : angle 5.25314 / 2.77 ( 2) hydrogen bonds : bond 0.05607 / 3.87 ( 496) hydrogen bonds : angle 5.14792 / 3.31 ( 1379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7526 (mt) REVERT: A 107 LYS cc_start: 0.8219 (tptm) cc_final: 0.7929 (tttt) REVERT: A 268 GLN cc_start: 0.5554 (mm-40) cc_final: 0.5063 (mt0) REVERT: A 426 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.4464 (t80) REVERT: A 471 LYS cc_start: 0.7760 (tmmt) cc_final: 0.7497 (tttp) REVERT: A 824 ASP cc_start: 0.8124 (p0) cc_final: 0.7906 (p0) REVERT: A 875 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (tp) REVERT: A 1133 LEU cc_start: 0.8316 (mp) cc_final: 0.7816 (tt) REVERT: A 1137 MET cc_start: 0.7344 (ttm) cc_final: 0.7003 (mtp) REVERT: C 184 GLU cc_start: 0.5606 (tm-30) cc_final: 0.5187 (tm-30) outliers start: 32 outliers final: 21 residues processed: 214 average time/residue: 0.0977 time to fit residues: 31.6728 Evaluate side-chains 200 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.201170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168398 restraints weight = 30027.817| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 4.09 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12478 Z= 0.193 Angle : 0.660 8.533 16915 Z= 0.357 Chirality : 0.046 0.206 1845 Planarity : 0.004 0.051 2077 Dihedral : 13.965 175.991 1927 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.31 % Favored : 90.54 % Rotamer: Outliers : 2.80 % Allowed : 14.76 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.22), residues: 1399 helix: 0.71 (0.22), residues: 587 sheet: -1.57 (0.41), residues: 144 loop : -2.72 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 155 TYR 0.022 0.002 TYR A1185 PHE 0.033 0.002 PHE A 173 TRP 0.011 0.002 TRP A 534 HIS 0.020 0.002 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (12477) covalent geometry : angle 0.65724 / 0.36 (16913) SS BOND : bond 0.00932 / 0.49 ( 1) SS BOND : angle 5.32206 / 2.80 ( 2) hydrogen bonds : bond 0.06493 / 4.46 ( 496) hydrogen bonds : angle 5.22849 / 3.37 ( 1379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7528 (mt) REVERT: A 107 LYS cc_start: 0.8206 (tptm) cc_final: 0.7938 (tttt) REVERT: A 268 GLN cc_start: 0.5619 (mm-40) cc_final: 0.5063 (mt0) REVERT: A 426 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.4542 (t80) REVERT: A 471 LYS cc_start: 0.7857 (tmmt) cc_final: 0.7581 (tttp) REVERT: A 824 ASP cc_start: 0.8101 (p0) cc_final: 0.7873 (p0) REVERT: A 875 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 1133 LEU cc_start: 0.8403 (mp) cc_final: 0.8048 (tp) REVERT: A 1137 MET cc_start: 0.7363 (ttm) cc_final: 0.7024 (mtp) REVERT: C 184 GLU cc_start: 0.5698 (tm-30) cc_final: 0.5415 (tm-30) outliers start: 35 outliers final: 30 residues processed: 205 average time/residue: 0.0999 time to fit residues: 31.0701 Evaluate side-chains 213 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0670 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 888 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.202871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170121 restraints weight = 21904.824| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.66 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12478 Z= 0.150 Angle : 0.622 8.446 16915 Z= 0.340 Chirality : 0.044 0.200 1845 Planarity : 0.004 0.054 2077 Dihedral : 13.941 176.928 1927 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.17 % Favored : 90.69 % Rotamer: Outliers : 2.87 % Allowed : 15.00 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.22), residues: 1399 helix: 0.84 (0.22), residues: 586 sheet: -1.43 (0.41), residues: 145 loop : -2.68 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 155 TYR 0.017 0.002 TYR C 197 PHE 0.035 0.002 PHE A1027 TRP 0.008 0.001 TRP A 362 HIS 0.012 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12477) covalent geometry : angle 0.61885 / 0.34 (16913) SS BOND : bond 0.00871 / 0.46 ( 1) SS BOND : angle 5.33394 / 2.81 ( 2) hydrogen bonds : bond 0.05942 / 4.09 ( 496) hydrogen bonds : angle 5.12854 / 3.30 ( 1379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 107 LYS cc_start: 0.8170 (tptm) cc_final: 0.7917 (ttpt) REVERT: A 268 GLN cc_start: 0.5583 (mm-40) cc_final: 0.5042 (mt0) REVERT: A 426 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.4500 (t80) REVERT: A 471 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7603 (tttp) REVERT: A 824 ASP cc_start: 0.8062 (p0) cc_final: 0.7847 (p0) REVERT: A 875 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 1133 LEU cc_start: 0.8329 (mp) cc_final: 0.8006 (tp) REVERT: A 1137 MET cc_start: 0.7323 (ttm) cc_final: 0.6968 (mtp) REVERT: C 184 GLU cc_start: 0.5627 (tm-30) cc_final: 0.5378 (tm-30) outliers start: 36 outliers final: 28 residues processed: 204 average time/residue: 0.1018 time to fit residues: 31.0846 Evaluate side-chains 209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 888 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170437 restraints weight = 28845.244| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 4.00 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12478 Z= 0.140 Angle : 0.618 8.542 16915 Z= 0.338 Chirality : 0.044 0.203 1845 Planarity : 0.004 0.053 2077 Dihedral : 13.908 177.196 1927 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.10 % Favored : 90.76 % Rotamer: Outliers : 2.87 % Allowed : 15.07 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1399 helix: 0.90 (0.22), residues: 586 sheet: -1.43 (0.41), residues: 145 loop : -2.64 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.017 0.001 TYR A 237 PHE 0.040 0.001 PHE A1027 TRP 0.008 0.001 TRP A 362 HIS 0.010 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12477) covalent geometry : angle 0.61538 / 0.34 (16913) SS BOND : bond 0.00869 / 0.46 ( 1) SS BOND : angle 5.19475 / 2.74 ( 2) hydrogen bonds : bond 0.05762 / 3.97 ( 496) hydrogen bonds : angle 5.10077 / 3.29 ( 1379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.472 Fit side-chains REVERT: A 99 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 107 LYS cc_start: 0.8124 (tptm) cc_final: 0.7896 (ttpt) REVERT: A 268 GLN cc_start: 0.5596 (mm-40) cc_final: 0.5049 (mt0) REVERT: A 426 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.4497 (t80) REVERT: A 471 LYS cc_start: 0.7734 (tmmt) cc_final: 0.7445 (tttp) REVERT: A 824 ASP cc_start: 0.8080 (p0) cc_final: 0.7864 (p0) REVERT: A 875 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 888 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: A 1133 LEU cc_start: 0.8283 (mp) cc_final: 0.7961 (tp) REVERT: A 1137 MET cc_start: 0.7284 (ttm) cc_final: 0.7046 (mtp) REVERT: B 134 LYS cc_start: 0.7099 (mttt) cc_final: 0.6712 (tttt) REVERT: C 184 GLU cc_start: 0.5591 (tm-30) cc_final: 0.5345 (tm-30) outliers start: 36 outliers final: 28 residues processed: 208 average time/residue: 0.1010 time to fit residues: 31.4046 Evaluate side-chains 211 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 3 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 overall best weight: 0.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 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 = 0.4324 r_free = 0.4324 target = 0.204610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167441 restraints weight = 20291.744| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 4.03 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12478 Z= 0.131 Angle : 0.610 8.593 16915 Z= 0.335 Chirality : 0.043 0.202 1845 Planarity : 0.004 0.053 2077 Dihedral : 13.874 177.670 1927 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.88 % Favored : 90.97 % Rotamer: Outliers : 2.10 % Allowed : 16.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1399 helix: 0.93 (0.22), residues: 588 sheet: -1.36 (0.41), residues: 145 loop : -2.62 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.018 0.001 TYR A 237 PHE 0.039 0.001 PHE A1027 TRP 0.010 0.001 TRP A 362 HIS 0.008 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12477) covalent geometry : angle 0.60695 / 0.33 (16913) SS BOND : bond 0.00897 / 0.47 ( 1) SS BOND : angle 5.17326 / 2.73 ( 2) hydrogen bonds : bond 0.05479 / 3.78 ( 496) hydrogen bonds : angle 5.03542 / 3.25 ( 1379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.538 Fit side-chains REVERT: A 99 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 107 LYS cc_start: 0.8138 (tptm) cc_final: 0.7921 (ttpt) REVERT: A 268 GLN cc_start: 0.5515 (mm-40) cc_final: 0.4876 (mt0) REVERT: A 426 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.4491 (t80) REVERT: A 471 LYS cc_start: 0.7711 (tmmt) cc_final: 0.7437 (tttp) REVERT: A 824 ASP cc_start: 0.8098 (p0) cc_final: 0.7885 (p0) REVERT: A 875 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8202 (tp) REVERT: A 1133 LEU cc_start: 0.8258 (mp) cc_final: 0.7993 (tp) REVERT: A 1137 MET cc_start: 0.7272 (ttm) cc_final: 0.7008 (mtp) REVERT: C 184 GLU cc_start: 0.5526 (tm-30) cc_final: 0.5197 (tm-30) outliers start: 26 outliers final: 22 residues processed: 201 average time/residue: 0.0965 time to fit residues: 29.2319 Evaluate side-chains 200 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.0570 chunk 132 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 888 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.207012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172711 restraints weight = 26280.839| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.99 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12478 Z= 0.125 Angle : 0.600 8.597 16915 Z= 0.328 Chirality : 0.042 0.198 1845 Planarity : 0.004 0.054 2077 Dihedral : 13.809 178.328 1927 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.33 % Rotamer: Outliers : 2.33 % Allowed : 15.93 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1399 helix: 1.03 (0.22), residues: 590 sheet: -1.27 (0.42), residues: 145 loop : -2.54 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.017 0.001 TYR A 237 PHE 0.034 0.001 PHE A1027 TRP 0.010 0.001 TRP A 362 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12477) covalent geometry : angle 0.59725 / 0.33 (16913) SS BOND : bond 0.00925 / 0.49 ( 1) SS BOND : angle 4.89189 / 2.58 ( 2) hydrogen bonds : bond 0.05060 / 3.49 ( 496) hydrogen bonds : angle 4.94177 / 3.18 ( 1379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.38 seconds wall clock time: 44 minutes 52.26 seconds (2692.26 seconds total)