Starting phenix.real_space_refine on Sat Aug 23 13:57:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_0704_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_0704_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_0704_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_0704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kl9_0704/08_2025/6kl9_0704.map" } 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-2.0-5787/lib/python3.9/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: 3.26, per 1000 atoms: 0.27 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: 0.58 Conformation dependent library (CDL) restraints added in 704.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.97 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: 1.64 Time building geometry restraints manager: 0.82 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=" 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=" C GLY A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.40e+00 bond pdb=" C TYR B 144 " pdb=" O TYR B 144 " ideal model delta sigma weight residual 1.237 1.217 0.020 1.19e-02 7.06e+03 2.74e+00 ... (remaining 12472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 16530 2.84 - 5.69: 318 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: 1685 0.099 - 0.198: 134 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: 1.040 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.070 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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= 0.248 Angle : 1.009 14.216 16915 Z= 0.607 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 aren 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 covalent geometry : bond 0.00458 (12477) covalent geometry : angle 1.00908 (16913) SS BOND : bond 0.00059 ( 1) SS BOND : angle 2.44960 ( 2) hydrogen bonds : bond 0.16885 ( 496) hydrogen bonds : angle 9.14442 ( 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 : 0.371 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: 0.7436 (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: 0.7007 (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: 0.6827 (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: 0.0996 time to fit residues: 51.4304 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 : 0.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 268 GLN A 577 ASN A 582 ASN A 803 ASN A 813 ASN A 955 ASN A 963 ASN A 989 GLN A1012 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.207577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175161 restraints weight = 30134.405| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 4.14 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 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 = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12478 Z= 0.151 Angle : 0.649 8.900 16915 Z= 0.353 Chirality : 0.045 0.265 1845 Planarity : 0.005 0.060 2077 Dihedral : 15.004 177.179 1991 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 2.49 % Allowed : 10.57 % Favored : 86.95 % 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 aren not related in a simple way. whole: -2.98 (0.19), residues: 1399 helix: -0.94 (0.19), residues: 589 sheet: -1.48 (0.46), residues: 122 loop : -3.10 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 43 TYR 0.021 0.002 TYR A1036 PHE 0.031 0.002 PHE A 173 TRP 0.019 0.002 TRP A1218 HIS 0.016 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00312 (12477) covalent geometry : angle 0.64709 (16913) SS BOND : bond 0.00674 ( 1) SS BOND : angle 5.12545 ( 2) hydrogen bonds : bond 0.05881 ( 496) hydrogen bonds : angle 5.62139 ( 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 243 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8081 (tptm) cc_final: 0.7793 (tttt) REVERT: A 268 GLN cc_start: 0.5418 (mm-40) cc_final: 0.4924 (mt0) REVERT: A 481 ASN cc_start: 0.7062 (p0) cc_final: 0.6858 (p0) REVERT: A 765 ILE cc_start: 0.6643 (pt) cc_final: 0.6244 (tp) REVERT: A 824 ASP cc_start: 0.7929 (p0) cc_final: 0.7717 (p0) REVERT: A 875 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 1035 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5866 (ttp) REVERT: A 1133 LEU cc_start: 0.8278 (mp) cc_final: 0.7988 (tt) REVERT: A 1137 MET cc_start: 0.7245 (ttm) cc_final: 0.7020 (mtp) REVERT: B 169 ASN cc_start: 0.7142 (t0) cc_final: 0.6882 (t0) REVERT: B 188 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8198 (t80) outliers start: 31 outliers final: 16 residues processed: 236 average time/residue: 0.0852 time to fit residues: 29.2898 Evaluate side-chains 190 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL 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 450 ASP 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 1035 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1132 SER 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 C residue 225 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 797 HIS C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.205454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172964 restraints weight = 33887.970| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 4.42 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12478 Z= 0.153 Angle : 0.622 8.716 16915 Z= 0.339 Chirality : 0.044 0.204 1845 Planarity : 0.004 0.052 2077 Dihedral : 14.128 177.141 1941 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 2.87 % Allowed : 11.34 % Favored : 85.78 % 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 aren not related in a simple way. whole: -2.10 (0.21), residues: 1399 helix: 0.12 (0.21), residues: 580 sheet: -1.49 (0.43), residues: 137 loop : -2.84 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 867 TYR 0.017 0.002 TYR A1185 PHE 0.060 0.002 PHE A1027 TRP 0.016 0.002 TRP A1218 HIS 0.016 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00339 (12477) covalent geometry : angle 0.61950 (16913) SS BOND : bond 0.01242 ( 1) SS BOND : angle 5.01231 ( 2) hydrogen bonds : bond 0.05886 ( 496) hydrogen bonds : angle 5.20885 ( 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 230 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7551 (mt) REVERT: A 107 LYS cc_start: 0.8231 (tptm) cc_final: 0.7954 (ttpt) REVERT: A 268 GLN cc_start: 0.5539 (mm-40) cc_final: 0.4954 (mt0) REVERT: A 471 LYS cc_start: 0.7784 (tmmt) cc_final: 0.7483 (tttp) REVERT: A 481 ASN cc_start: 0.7182 (p0) cc_final: 0.6886 (p0) REVERT: A 824 ASP cc_start: 0.7993 (p0) cc_final: 0.7779 (p0) REVERT: A 875 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 1133 LEU cc_start: 0.8247 (mp) cc_final: 0.7938 (tt) REVERT: A 1137 MET cc_start: 0.7278 (ttm) cc_final: 0.7011 (mtp) REVERT: B 188 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (t80) REVERT: C 196 PHE cc_start: 0.6369 (m-10) cc_final: 0.6125 (m-10) outliers start: 36 outliers final: 25 residues processed: 217 average time/residue: 0.0829 time to fit residues: 26.8717 Evaluate side-chains 197 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 SER 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 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 802 ILE 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 888 GLN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1132 SER 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 188 TYR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 26 optimal weight: 0.0770 chunk 92 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 126 optimal weight: 0.0270 chunk 21 optimal weight: 6.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 793 GLN C 145 ASN C 193 GLN C 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176568 restraints weight = 29773.868| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 4.36 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12478 Z= 0.116 Angle : 0.570 8.966 16915 Z= 0.311 Chirality : 0.042 0.185 1845 Planarity : 0.004 0.047 2077 Dihedral : 13.929 179.077 1935 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.52 % Favored : 92.34 % Rotamer: Outliers : 1.94 % Allowed : 12.28 % Favored : 85.78 % 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 aren not related in a simple way. whole: -1.57 (0.22), residues: 1399 helix: 0.75 (0.22), residues: 582 sheet: -1.54 (0.41), residues: 147 loop : -2.68 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 867 TYR 0.018 0.001 TYR A1036 PHE 0.031 0.001 PHE A 173 TRP 0.012 0.001 TRP A1086 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00240 (12477) covalent geometry : angle 0.56819 (16913) SS BOND : bond 0.00971 ( 1) SS BOND : angle 3.91222 ( 2) hydrogen bonds : bond 0.04625 ( 496) hydrogen bonds : angle 4.77241 ( 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 228 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7541 (mt) REVERT: A 107 LYS cc_start: 0.8223 (tptm) cc_final: 0.7972 (tttt) REVERT: A 268 GLN cc_start: 0.5368 (mm-40) cc_final: 0.4809 (mt0) REVERT: A 471 LYS cc_start: 0.7720 (tmmt) cc_final: 0.7504 (tttp) REVERT: A 765 ILE cc_start: 0.6601 (pt) cc_final: 0.6124 (tp) REVERT: A 875 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 883 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7505 (ttm170) REVERT: A 1137 MET cc_start: 0.7233 (ttm) cc_final: 0.6890 (mtp) REVERT: B 221 GLU cc_start: 0.7880 (mp0) cc_final: 0.7678 (mp0) REVERT: C 196 PHE cc_start: 0.6448 (m-80) cc_final: 0.6019 (m-10) outliers start: 24 outliers final: 15 residues processed: 219 average time/residue: 0.0832 time to fit residues: 27.2379 Evaluate side-chains 195 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN 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 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: 0.3980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 793 GLN A 873 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.206837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.173915 restraints weight = 23476.830| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.78 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12478 Z= 0.135 Angle : 0.592 9.914 16915 Z= 0.320 Chirality : 0.043 0.205 1845 Planarity : 0.004 0.046 2077 Dihedral : 13.810 177.036 1929 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.17 % Favored : 91.69 % Rotamer: Outliers : 2.41 % Allowed : 13.83 % Favored : 83.76 % 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 aren not related in a simple way. whole: -1.35 (0.22), residues: 1399 helix: 0.96 (0.22), residues: 581 sheet: -1.39 (0.42), residues: 145 loop : -2.59 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 867 TYR 0.016 0.001 TYR C 121 PHE 0.026 0.001 PHE A 173 TRP 0.017 0.002 TRP A1086 HIS 0.013 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00293 (12477) covalent geometry : angle 0.59104 (16913) SS BOND : bond 0.00958 ( 1) SS BOND : angle 3.71202 ( 2) hydrogen bonds : bond 0.05165 ( 496) hydrogen bonds : angle 4.83460 ( 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 217 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 107 LYS cc_start: 0.8093 (tptm) cc_final: 0.7892 (tttt) REVERT: A 268 GLN cc_start: 0.5271 (mm-40) cc_final: 0.4828 (mt0) REVERT: A 387 LYS cc_start: 0.7287 (mptt) cc_final: 0.6671 (mmmt) REVERT: A 471 LYS cc_start: 0.7830 (tmmt) cc_final: 0.7622 (tttp) REVERT: A 875 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8194 (tp) outliers start: 30 outliers final: 22 residues processed: 205 average time/residue: 0.0811 time to fit residues: 24.8097 Evaluate side-chains 196 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 SER 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 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 888 GLN 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 Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 HIS C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167516 restraints weight = 29248.362| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.22 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 = 0.34 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12478 Z= 0.189 Angle : 0.642 8.646 16915 Z= 0.348 Chirality : 0.046 0.215 1845 Planarity : 0.004 0.048 2077 Dihedral : 13.909 175.737 1929 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.17 % Favored : 90.69 % Rotamer: Outliers : 3.11 % Allowed : 14.14 % Favored : 82.75 % 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 aren not related in a simple way. whole: -1.36 (0.22), residues: 1399 helix: 0.98 (0.22), residues: 581 sheet: -1.48 (0.42), residues: 141 loop : -2.58 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 867 TYR 0.022 0.002 TYR A1185 PHE 0.030 0.002 PHE A1027 TRP 0.017 0.002 TRP A1086 HIS 0.020 0.002 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00430 (12477) covalent geometry : angle 0.64146 (16913) SS BOND : bond 0.00898 ( 1) SS BOND : angle 3.36837 ( 2) hydrogen bonds : bond 0.06315 ( 496) hydrogen bonds : angle 5.02504 ( 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 233 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7516 (mt) REVERT: A 189 ILE cc_start: 0.7801 (mt) cc_final: 0.7593 (mt) REVERT: A 268 GLN cc_start: 0.5374 (mm-40) cc_final: 0.5051 (mt0) REVERT: A 401 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7029 (tt0) REVERT: A 426 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.4743 (t80) REVERT: A 471 LYS cc_start: 0.7930 (tmmt) cc_final: 0.7708 (tttp) REVERT: A 530 PHE cc_start: 0.7776 (t80) cc_final: 0.7557 (t80) REVERT: A 875 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8161 (tp) outliers start: 39 outliers final: 31 residues processed: 220 average time/residue: 0.0816 time to fit residues: 27.0035 Evaluate side-chains 209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 368 ASP 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 470 ILE Chi-restraints excluded: chain A residue 485 SER 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 835 GLU 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 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 873 HIS A 888 GLN B 163 GLN C 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168977 restraints weight = 30235.127| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.24 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12478 Z= 0.175 Angle : 0.635 8.643 16915 Z= 0.345 Chirality : 0.045 0.211 1845 Planarity : 0.004 0.049 2077 Dihedral : 13.912 176.245 1929 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.95 % Favored : 90.90 % Rotamer: Outliers : 2.87 % Allowed : 14.84 % Favored : 82.28 % 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 aren not related in a simple way. whole: -1.34 (0.22), residues: 1399 helix: 1.01 (0.22), residues: 570 sheet: -1.60 (0.41), residues: 145 loop : -2.50 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 867 TYR 0.018 0.002 TYR A1185 PHE 0.031 0.002 PHE A 173 TRP 0.015 0.002 TRP A1086 HIS 0.018 0.002 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00394 (12477) covalent geometry : angle 0.63429 (16913) SS BOND : bond 0.00888 ( 1) SS BOND : angle 3.31398 ( 2) hydrogen bonds : bond 0.06092 ( 496) hydrogen bonds : angle 5.02941 ( 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 225 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 189 ILE cc_start: 0.7810 (mt) cc_final: 0.7601 (mt) REVERT: A 268 GLN cc_start: 0.5405 (mm-40) cc_final: 0.5100 (mt0) REVERT: A 278 LYS cc_start: 0.7385 (pttp) cc_final: 0.7119 (mtpp) REVERT: A 401 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7089 (tt0) REVERT: A 403 TYR cc_start: 0.6076 (m-80) cc_final: 0.5832 (m-80) REVERT: A 426 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.4719 (t80) REVERT: A 471 LYS cc_start: 0.7832 (tmmt) cc_final: 0.7601 (tttp) REVERT: A 530 PHE cc_start: 0.7927 (t80) cc_final: 0.7670 (t80) REVERT: A 875 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8150 (tp) REVERT: A 1023 ASP cc_start: 0.6709 (m-30) cc_final: 0.6382 (m-30) outliers start: 36 outliers final: 32 residues processed: 214 average time/residue: 0.0864 time to fit residues: 27.6276 Evaluate side-chains 211 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER 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 470 ILE Chi-restraints excluded: chain A residue 485 SER 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 835 GLU 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 1021 ILE Chi-restraints excluded: chain A residue 1219 LEU 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 213 VAL 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: 0.7980 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 306 ASN A 340 ASN A 873 HIS C 125 GLN C 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.201195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.167106 restraints weight = 22029.955| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.87 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12478 Z= 0.180 Angle : 0.659 8.312 16915 Z= 0.356 Chirality : 0.045 0.214 1845 Planarity : 0.004 0.064 2077 Dihedral : 13.939 175.732 1929 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.46 % Favored : 90.40 % Rotamer: Outliers : 3.50 % Allowed : 14.61 % Favored : 81.90 % 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 aren not related in a simple way. whole: -1.33 (0.22), residues: 1399 helix: 1.03 (0.22), residues: 570 sheet: -1.54 (0.40), residues: 150 loop : -2.54 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 230 TYR 0.020 0.002 TYR A1185 PHE 0.063 0.002 PHE A1027 TRP 0.014 0.001 TRP A1086 HIS 0.018 0.002 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00408 (12477) covalent geometry : angle 0.65806 (16913) SS BOND : bond 0.00836 ( 1) SS BOND : angle 3.17993 ( 2) hydrogen bonds : bond 0.06176 ( 496) hydrogen bonds : angle 5.03311 ( 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 229 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 189 ILE cc_start: 0.7824 (mt) cc_final: 0.7615 (mt) REVERT: A 268 GLN cc_start: 0.5381 (mm-40) cc_final: 0.4866 (mm-40) REVERT: A 278 LYS cc_start: 0.7369 (pttp) cc_final: 0.7059 (mtpp) REVERT: A 401 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7089 (tt0) REVERT: A 403 TYR cc_start: 0.6035 (m-80) cc_final: 0.5724 (m-80) REVERT: A 426 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.4640 (t80) REVERT: A 471 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7598 (tttp) REVERT: A 530 PHE cc_start: 0.8056 (t80) cc_final: 0.7841 (t80) REVERT: A 875 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8263 (tp) REVERT: C 184 GLU cc_start: 0.5937 (tp30) cc_final: 0.5671 (tm-30) REVERT: C 186 MET cc_start: 0.6564 (pmm) cc_final: 0.6270 (pmm) outliers start: 44 outliers final: 36 residues processed: 218 average time/residue: 0.0779 time to fit residues: 25.5484 Evaluate side-chains 217 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER 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 470 ILE Chi-restraints excluded: chain A residue 485 SER 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 835 GLU 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 889 ASN Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1219 LEU 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 158 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 HIS C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171504 restraints weight = 28986.220| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 4.09 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) = 0.171 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12478 Z= 0.145 Angle : 0.623 8.863 16915 Z= 0.335 Chirality : 0.044 0.253 1845 Planarity : 0.004 0.052 2077 Dihedral : 13.865 177.189 1929 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 2.95 % Allowed : 15.23 % Favored : 81.82 % 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 aren not related in a simple way. whole: -1.13 (0.22), residues: 1399 helix: 1.18 (0.22), residues: 571 sheet: -1.17 (0.46), residues: 125 loop : -2.45 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 230 TYR 0.018 0.001 TYR A1036 PHE 0.038 0.001 PHE A1027 TRP 0.014 0.001 TRP A1086 HIS 0.012 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00320 (12477) covalent geometry : angle 0.62208 (16913) SS BOND : bond 0.00807 ( 1) SS BOND : angle 3.08379 ( 2) hydrogen bonds : bond 0.05512 ( 496) hydrogen bonds : angle 4.89429 ( 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 219 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7584 (mt) REVERT: A 189 ILE cc_start: 0.7819 (mt) cc_final: 0.7604 (mt) REVERT: A 268 GLN cc_start: 0.5493 (mm-40) cc_final: 0.5207 (mm-40) REVERT: A 278 LYS cc_start: 0.7369 (pttp) cc_final: 0.7070 (mtpp) REVERT: A 401 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7102 (tt0) REVERT: A 403 TYR cc_start: 0.5970 (m-80) cc_final: 0.5645 (m-80) REVERT: A 426 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.4582 (t80) REVERT: A 471 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7491 (tttp) REVERT: A 530 PHE cc_start: 0.7900 (t80) cc_final: 0.7694 (t80) REVERT: A 875 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8093 (tp) REVERT: C 137 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6448 (t0) outliers start: 37 outliers final: 32 residues processed: 210 average time/residue: 0.0793 time to fit residues: 25.1350 Evaluate side-chains 209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 312 SER 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 485 SER 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 835 GLU 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 1014 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1219 LEU 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 158 VAL Chi-restraints excluded: chain C residue 213 VAL 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: 0.6980 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.0030 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 873 HIS C 193 GLN C 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172947 restraints weight = 20125.205| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.60 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12478 Z= 0.136 Angle : 0.615 8.860 16915 Z= 0.331 Chirality : 0.044 0.219 1845 Planarity : 0.004 0.053 2077 Dihedral : 13.827 177.373 1929 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.74 % Favored : 91.12 % Rotamer: Outliers : 2.87 % Allowed : 15.62 % Favored : 81.51 % 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 aren not related in a simple way. whole: -1.06 (0.23), residues: 1399 helix: 1.25 (0.22), residues: 570 sheet: -1.27 (0.42), residues: 145 loop : -2.39 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 230 TYR 0.016 0.001 TYR C 121 PHE 0.039 0.001 PHE A1027 TRP 0.017 0.001 TRP A1193 HIS 0.011 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00297 (12477) covalent geometry : angle 0.61416 (16913) SS BOND : bond 0.00831 ( 1) SS BOND : angle 3.11876 ( 2) hydrogen bonds : bond 0.05286 ( 496) hydrogen bonds : angle 4.85124 ( 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 220 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7502 (mt) REVERT: A 189 ILE cc_start: 0.7853 (mt) cc_final: 0.7605 (mt) REVERT: A 268 GLN cc_start: 0.5363 (mm-40) cc_final: 0.5068 (mm-40) REVERT: A 387 LYS cc_start: 0.7190 (mptt) cc_final: 0.6597 (mmmt) REVERT: A 401 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7106 (tt0) REVERT: A 403 TYR cc_start: 0.5909 (m-80) cc_final: 0.5593 (m-80) REVERT: A 426 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.4523 (t80) REVERT: A 471 LYS cc_start: 0.7732 (tmmt) cc_final: 0.7478 (tttp) REVERT: A 530 PHE cc_start: 0.7950 (t80) cc_final: 0.7700 (t80) REVERT: A 875 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 1098 LEU cc_start: 0.7745 (tp) cc_final: 0.7389 (tt) REVERT: C 137 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6587 (t0) outliers start: 36 outliers final: 29 residues processed: 209 average time/residue: 0.0873 time to fit residues: 27.1316 Evaluate side-chains 212 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER 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 485 SER 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 835 GLU 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 1132 SER Chi-restraints excluded: chain A residue 1219 LEU 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 158 VAL Chi-restraints excluded: chain C residue 213 VAL 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 873 HIS C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.203369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169595 restraints weight = 24887.958| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.96 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12478 Z= 0.146 Angle : 0.625 8.892 16915 Z= 0.335 Chirality : 0.044 0.207 1845 Planarity : 0.004 0.055 2077 Dihedral : 13.828 176.825 1929 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 2.87 % Allowed : 15.93 % Favored : 81.20 % 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 aren not related in a simple way. whole: -1.00 (0.22), residues: 1399 helix: 1.26 (0.22), residues: 571 sheet: -1.09 (0.46), residues: 125 loop : -2.35 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 230 TYR 0.023 0.002 TYR A 277 PHE 0.037 0.001 PHE A1027 TRP 0.016 0.001 TRP A1193 HIS 0.013 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00326 (12477) covalent geometry : angle 0.62422 (16913) SS BOND : bond 0.00845 ( 1) SS BOND : angle 3.10414 ( 2) hydrogen bonds : bond 0.05445 ( 496) hydrogen bonds : angle 4.87025 ( 1379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.58 seconds wall clock time: 35 minutes 0.88 seconds (2100.88 seconds total)