Starting phenix.real_space_refine on Sat Sep 12 13:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4h_14497/09_2026/7z4h_14497.cif" } resolution = 3.49 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2494 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 139 5.49 5 S 23 5.16 5 C 8327 2.51 5 N 2435 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1970 Classifications: {'RNAv2': 92} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 49, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 625 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 10916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10916 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 35, 'TRANS': 1298} Chain breaks: 5 Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 13900 At special positions: 0 Unit cell: (98.8, 120.9, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 139 15.00 O 2976 8.00 N 2435 7.00 C 8327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 640.5 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 55.8% alpha, 8.4% beta 51 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.568A pdb=" N LYS B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.593A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.519A pdb=" N GLN B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.457A pdb=" N ASN B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.963A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.653A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.576A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.095A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.575A pdb=" N LYS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.184A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.713A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.894A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.314A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 777 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 829 through 833 Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.603A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.754A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 902 through 906 removed outlier: 3.511A pdb=" N GLY B 906 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.870A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.907A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.377A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.564A pdb=" N PHE B1046 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.543A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1185 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1249 through 1264 Processing helix chain 'B' and resid 1265 through 1281 removed outlier: 3.701A pdb=" N ILE B1269 " --> pdb=" O TYR B1265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 4.292A pdb=" N MET B 763 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.788A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.422A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.952A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 528 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 839 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.558A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 515 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2941 1.33 - 1.45: 3731 1.45 - 1.57: 7455 1.57 - 1.69: 277 1.69 - 1.81: 44 Bond restraints: 14448 Sorted by residual: bond pdb=" C1' DT C 11 " pdb=" N1 DT C 11 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C1' DC C 10 " pdb=" N1 DC C 10 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.49e+00 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.60e+00 bond pdb=" C3' DA D 4 " pdb=" C2' DA D 4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.22e+00 bond pdb=" C3' DT D 5 " pdb=" C2' DT D 5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.10e+00 ... (remaining 14443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19622 1.96 - 3.92: 451 3.92 - 5.87: 32 5.87 - 7.83: 0 7.83 - 9.79: 1 Bond angle restraints: 20106 Sorted by residual: angle pdb=" O4' DC C 2 " pdb=" C4' DC C 2 " pdb=" C3' DC C 2 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DC D -20 " pdb=" C4' DC D -20 " pdb=" C3' DC D -20 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 ... (remaining 20101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7640 17.94 - 35.88: 463 35.88 - 53.82: 257 53.82 - 71.76: 101 71.76 - 89.70: 10 Dihedral angle restraints: 8471 sinusoidal: 4547 harmonic: 3924 Sorted by residual: dihedral pdb=" C4' G A 43 " pdb=" C3' G A 43 " pdb=" C2' G A 43 " pdb=" C1' G A 43 " ideal model delta sinusoidal sigma weight residual 36.34 -36.81 73.15 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' A A 88 " pdb=" C3' A A 88 " pdb=" C2' A A 88 " pdb=" C1' A A 88 " ideal model delta sinusoidal sigma weight residual 36.35 -36.56 72.90 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' G A 89 " pdb=" C3' G A 89 " pdb=" C2' G A 89 " pdb=" C1' G A 89 " ideal model delta sinusoidal sigma weight residual 36.34 -36.27 72.62 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 8468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1929 0.058 - 0.115: 244 0.115 - 0.173: 14 0.173 - 0.230: 68 0.230 - 0.288: 46 Chirality restraints: 2301 Sorted by residual: chirality pdb=" C2' U A 90 " pdb=" C3' U A 90 " pdb=" O2' U A 90 " pdb=" C1' U A 90 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" P U A 44 " pdb=" OP1 U A 44 " pdb=" OP2 U A 44 " pdb=" O5' U A 44 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' G A 81 " pdb=" C3' G A 81 " pdb=" O2' G A 81 " pdb=" C1' G A 81 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2298 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 42 " -0.026 2.00e-02 2.50e+03 1.17e-02 3.79e+00 pdb=" N9 A A 42 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A A 42 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 42 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 42 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A 42 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A A 42 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 42 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 42 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 294 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LYS B 294 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS B 294 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN B 295 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 295 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN B 295 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN B 295 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 296 " 0.009 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 182 2.61 - 3.19: 12046 3.19 - 3.76: 24087 3.76 - 4.33: 32186 4.33 - 4.90: 48769 Nonbonded interactions: 117270 Sorted by model distance: nonbonded pdb=" O2' U A 44 " pdb=" OE1 GLN B 402 " model vdw 2.043 3.040 nonbonded pdb=" ND2 ASN B 240 " pdb=" OD1 ASN B 255 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASP B 853 " pdb=" OG1 THR B 893 " model vdw 2.213 3.040 nonbonded pdb=" OE2 GLU B 762 " pdb=" OG SER B 960 " model vdw 2.222 3.040 nonbonded pdb=" O GLN B 817 " pdb=" OH TYR B 882 " model vdw 2.226 3.040 ... (remaining 117265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.890 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.003 0.046 14448 Z= 0.240 Angle : 0.605 9.791 20106 Z= 0.378 Chirality : 0.064 0.288 2301 Planarity : 0.003 0.031 2055 Dihedral : 15.440 89.704 5929 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 4.92 % Favored : 93.82 % 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 are not related in a simple way. whole: 1.67 (0.24), residues: 1322 helix: 2.32 (0.21), residues: 650 sheet: -0.32 (0.59), residues: 89 loop : -0.01 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.010 0.001 TYR B 347 PHE 0.010 0.001 PHE B1008 TRP 0.007 0.001 TRP B 18 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.24 (14448) covalent geometry : angle 0.60471 / 0.38 (20106) hydrogen bonds : bond 0.12964 / 6.81 ( 641) hydrogen bonds : angle 5.55070 / 2.30 ( 1721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8371 (p) REVERT: B 410 ILE cc_start: 0.9531 (mt) cc_final: 0.9313 (pt) REVERT: B 587 PHE cc_start: 0.8169 (m-80) cc_final: 0.7775 (m-10) REVERT: B 620 VAL cc_start: 0.9706 (t) cc_final: 0.9487 (p) REVERT: B 631 MET cc_start: 0.9098 (mmm) cc_final: 0.8821 (mmp) REVERT: B 654 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7778 (tpm170) REVERT: B 703 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8693 (t) REVERT: B 745 ASP cc_start: 0.8887 (t70) cc_final: 0.8360 (m-30) REVERT: B 933 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9127 (tm-30) REVERT: B 1037 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6465 (t80) REVERT: B 1272 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9289 (mt0) outliers start: 15 outliers final: 2 residues processed: 139 average time/residue: 0.1471 time to fit residues: 28.5606 Evaluate side-chains 70 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1272 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.059886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.038529 restraints weight = 83961.353| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 5.93 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14448 Z= 0.252 Angle : 0.940 22.436 20106 Z= 0.416 Chirality : 0.084 1.342 2301 Planarity : 0.004 0.047 2055 Dihedral : 17.188 131.105 3113 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.50 % Allowed : 8.85 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1322 helix: 2.42 (0.21), residues: 648 sheet: -0.06 (0.59), residues: 85 loop : -0.10 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 629 TYR 0.015 0.002 TYR B1242 PHE 0.012 0.001 PHE B 575 TRP 0.008 0.001 TRP B 18 HIS 0.009 0.001 HIS B1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 (14448) covalent geometry : angle 0.94025 / 0.42 (20106) hydrogen bonds : bond 0.04500 / 2.34 ( 641) hydrogen bonds : angle 4.68042 / 1.93 ( 1721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9436 (mmt) cc_final: 0.9187 (tpp) REVERT: B 587 PHE cc_start: 0.8357 (m-80) cc_final: 0.7948 (m-10) REVERT: B 623 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9197 (tp) REVERT: B 631 MET cc_start: 0.9088 (mmm) cc_final: 0.8823 (mmp) REVERT: B 745 ASP cc_start: 0.8766 (t70) cc_final: 0.8423 (m-30) REVERT: B 933 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9091 (tm-30) outliers start: 18 outliers final: 8 residues processed: 77 average time/residue: 0.1414 time to fit residues: 15.6313 Evaluate side-chains 64 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.0470 chunk 136 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 87 optimal weight: 0.0070 chunk 132 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039521 restraints weight = 83133.723| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 6.11 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 14448 Z= 0.131 Angle : 0.700 16.123 20106 Z= 0.323 Chirality : 0.061 0.865 2301 Planarity : 0.003 0.044 2055 Dihedral : 17.094 142.862 3098 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.92 % Allowed : 8.85 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1322 helix: 2.48 (0.21), residues: 643 sheet: -0.06 (0.56), residues: 87 loop : -0.03 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 653 TYR 0.015 0.001 TYR B 812 PHE 0.024 0.001 PHE B 569 TRP 0.007 0.001 TRP B 883 HIS 0.017 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14448) covalent geometry : angle 0.69982 / 0.32 (20106) hydrogen bonds : bond 0.03515 / 1.82 ( 641) hydrogen bonds : angle 4.40884 / 1.83 ( 1721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9263 (mm) REVERT: B 587 PHE cc_start: 0.8389 (m-80) cc_final: 0.7928 (m-10) REVERT: B 631 MET cc_start: 0.9100 (mmm) cc_final: 0.8810 (mmp) REVERT: B 745 ASP cc_start: 0.8754 (t70) cc_final: 0.8385 (m-30) REVERT: B 933 GLN cc_start: 0.9288 (tm-30) cc_final: 0.9068 (tm-30) REVERT: B 1037 PHE cc_start: 0.7312 (t80) cc_final: 0.7111 (t80) outliers start: 23 outliers final: 12 residues processed: 75 average time/residue: 0.1238 time to fit residues: 13.7919 Evaluate side-chains 66 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1039 TYR Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.060163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.038635 restraints weight = 84567.466| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 6.10 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14448 Z= 0.163 Angle : 0.666 12.897 20106 Z= 0.312 Chirality : 0.053 0.675 2301 Planarity : 0.003 0.045 2055 Dihedral : 17.057 136.964 3098 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.09 % Allowed : 9.35 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1322 helix: 2.48 (0.21), residues: 646 sheet: -0.22 (0.55), residues: 87 loop : 0.04 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 783 TYR 0.011 0.001 TYR B 812 PHE 0.015 0.001 PHE B 575 TRP 0.018 0.001 TRP B 883 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (14448) covalent geometry : angle 0.66613 / 0.31 (20106) hydrogen bonds : bond 0.03557 / 1.83 ( 641) hydrogen bonds : angle 4.31270 / 1.80 ( 1721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.9035 (mtp) cc_final: 0.8101 (mmm) REVERT: B 296 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9324 (mm) REVERT: B 587 PHE cc_start: 0.8426 (m-80) cc_final: 0.7979 (m-10) REVERT: B 745 ASP cc_start: 0.8757 (t70) cc_final: 0.8445 (m-30) REVERT: B 933 GLN cc_start: 0.9309 (tm-30) cc_final: 0.9074 (tm-30) REVERT: B 1037 PHE cc_start: 0.7322 (t80) cc_final: 0.7030 (t80) outliers start: 25 outliers final: 15 residues processed: 75 average time/residue: 0.1155 time to fit residues: 13.2325 Evaluate side-chains 68 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 121 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.038784 restraints weight = 84444.823| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 6.03 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14448 Z= 0.139 Angle : 0.620 12.319 20106 Z= 0.292 Chirality : 0.050 0.532 2301 Planarity : 0.003 0.043 2055 Dihedral : 17.056 135.470 3098 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.50 % Allowed : 10.18 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1322 helix: 2.49 (0.21), residues: 647 sheet: -0.22 (0.55), residues: 87 loop : 0.02 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 783 TYR 0.010 0.001 TYR B 656 PHE 0.014 0.001 PHE B 575 TRP 0.010 0.001 TRP B 883 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (14448) covalent geometry : angle 0.61998 / 0.29 (20106) hydrogen bonds : bond 0.03267 / 1.69 ( 641) hydrogen bonds : angle 4.23398 / 1.78 ( 1721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9328 (mm) REVERT: B 383 MET cc_start: 0.8832 (tpp) cc_final: 0.8467 (tpp) REVERT: B 534 MET cc_start: 0.6385 (ppp) cc_final: 0.6168 (ppp) REVERT: B 587 PHE cc_start: 0.8516 (m-80) cc_final: 0.7469 (m-80) REVERT: B 631 MET cc_start: 0.9138 (mmm) cc_final: 0.8701 (mtp) REVERT: B 745 ASP cc_start: 0.8772 (t70) cc_final: 0.8419 (m-30) REVERT: B 933 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9025 (tm-30) REVERT: B 1037 PHE cc_start: 0.7264 (t80) cc_final: 0.6977 (t80) outliers start: 18 outliers final: 14 residues processed: 68 average time/residue: 0.1092 time to fit residues: 11.4075 Evaluate side-chains 67 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038789 restraints weight = 83513.869| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 6.00 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14448 Z= 0.128 Angle : 0.603 10.361 20106 Z= 0.285 Chirality : 0.049 0.475 2301 Planarity : 0.003 0.042 2055 Dihedral : 17.041 134.311 3098 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.50 % Allowed : 10.18 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1322 helix: 2.55 (0.21), residues: 646 sheet: -0.23 (0.54), residues: 92 loop : 0.05 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.015 0.001 TYR B 812 PHE 0.011 0.001 PHE B1008 TRP 0.050 0.002 TRP B 883 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (14448) covalent geometry : angle 0.60279 / 0.29 (20106) hydrogen bonds : bond 0.03251 / 1.68 ( 641) hydrogen bonds : angle 4.21333 / 1.80 ( 1721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9332 (mm) REVERT: B 383 MET cc_start: 0.8799 (tpp) cc_final: 0.8334 (tpp) REVERT: B 534 MET cc_start: 0.6515 (ppp) cc_final: 0.6285 (ppp) REVERT: B 564 LEU cc_start: 0.9716 (mt) cc_final: 0.9456 (pp) REVERT: B 587 PHE cc_start: 0.8329 (m-80) cc_final: 0.7944 (m-80) REVERT: B 631 MET cc_start: 0.9148 (mmm) cc_final: 0.8719 (mtp) REVERT: B 745 ASP cc_start: 0.8739 (t70) cc_final: 0.8393 (m-30) REVERT: B 933 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9026 (tm-30) REVERT: B 1037 PHE cc_start: 0.7184 (t80) cc_final: 0.6847 (t80) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.1203 time to fit residues: 13.0667 Evaluate side-chains 66 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 115 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 142 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 3.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037714 restraints weight = 85149.179| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 6.03 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14448 Z= 0.182 Angle : 0.631 10.129 20106 Z= 0.299 Chirality : 0.049 0.475 2301 Planarity : 0.003 0.042 2055 Dihedral : 17.088 135.081 3098 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.75 % Allowed : 9.93 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1322 helix: 2.49 (0.21), residues: 647 sheet: -0.45 (0.54), residues: 87 loop : 0.05 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 780 TYR 0.013 0.001 TYR B 812 PHE 0.010 0.001 PHE B1134 TRP 0.041 0.002 TRP B 883 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (14448) covalent geometry : angle 0.63140 / 0.30 (20106) hydrogen bonds : bond 0.03487 / 1.80 ( 641) hydrogen bonds : angle 4.23273 / 1.81 ( 1721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8969 (mtp) cc_final: 0.8149 (mmm) REVERT: B 296 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9340 (mm) REVERT: B 383 MET cc_start: 0.8855 (tpp) cc_final: 0.8484 (tpp) REVERT: B 534 MET cc_start: 0.6640 (ppp) cc_final: 0.6402 (ppp) REVERT: B 587 PHE cc_start: 0.8450 (m-80) cc_final: 0.7817 (m-80) REVERT: B 631 MET cc_start: 0.9156 (mmm) cc_final: 0.8732 (mtp) REVERT: B 662 LEU cc_start: 0.8949 (mt) cc_final: 0.8569 (pp) REVERT: B 933 GLN cc_start: 0.9350 (tm-30) cc_final: 0.9042 (tm-30) REVERT: B 1037 PHE cc_start: 0.7321 (t80) cc_final: 0.6988 (t80) outliers start: 21 outliers final: 16 residues processed: 71 average time/residue: 0.1317 time to fit residues: 13.8622 Evaluate side-chains 67 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 93 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037340 restraints weight = 84350.262| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 5.83 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14448 Z= 0.216 Angle : 0.669 10.292 20106 Z= 0.318 Chirality : 0.050 0.512 2301 Planarity : 0.004 0.066 2055 Dihedral : 17.132 135.083 3098 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.09 % Allowed : 10.02 % Favored : 87.90 % 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 are not related in a simple way. whole: 1.63 (0.24), residues: 1322 helix: 2.31 (0.21), residues: 655 sheet: -0.79 (0.53), residues: 97 loop : 0.02 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 215 TYR 0.015 0.001 TYR B 136 PHE 0.011 0.001 PHE B1204 TRP 0.046 0.002 TRP B 883 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (14448) covalent geometry : angle 0.66942 / 0.32 (20106) hydrogen bonds : bond 0.03700 / 1.90 ( 641) hydrogen bonds : angle 4.33448 / 1.85 ( 1721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.9022 (mtp) cc_final: 0.8206 (mmm) REVERT: B 296 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 383 MET cc_start: 0.8915 (tpp) cc_final: 0.8494 (tpp) REVERT: B 587 PHE cc_start: 0.8714 (m-80) cc_final: 0.8364 (m-80) REVERT: B 631 MET cc_start: 0.9169 (mmm) cc_final: 0.8770 (mtp) REVERT: B 656 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7017 (p90) REVERT: B 933 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9054 (tm-30) REVERT: B 1037 PHE cc_start: 0.7348 (t80) cc_final: 0.6995 (t80) REVERT: B 1333 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8558 (ptt180) outliers start: 25 outliers final: 20 residues processed: 72 average time/residue: 0.1257 time to fit residues: 13.5699 Evaluate side-chains 72 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.058865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037279 restraints weight = 84389.523| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 5.95 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14448 Z= 0.186 Angle : 0.648 13.595 20106 Z= 0.307 Chirality : 0.049 0.509 2301 Planarity : 0.003 0.044 2055 Dihedral : 17.024 134.792 3098 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.92 % Allowed : 10.52 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1322 helix: 2.25 (0.21), residues: 661 sheet: -0.74 (0.53), residues: 97 loop : 0.07 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 780 TYR 0.019 0.001 TYR B 812 PHE 0.011 0.001 PHE B 970 TRP 0.040 0.002 TRP B 883 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (14448) covalent geometry : angle 0.64847 / 0.31 (20106) hydrogen bonds : bond 0.03527 / 1.82 ( 641) hydrogen bonds : angle 4.28314 / 1.83 ( 1721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.9003 (mtp) cc_final: 0.8162 (mmm) REVERT: B 296 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9374 (mm) REVERT: B 383 MET cc_start: 0.8945 (tpp) cc_final: 0.8478 (tpp) REVERT: B 587 PHE cc_start: 0.8719 (m-80) cc_final: 0.8491 (m-80) REVERT: B 631 MET cc_start: 0.9168 (mmm) cc_final: 0.8785 (mtp) REVERT: B 656 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7025 (p90) REVERT: B 933 GLN cc_start: 0.9404 (tm-30) cc_final: 0.9080 (tm-30) REVERT: B 1037 PHE cc_start: 0.7439 (t80) cc_final: 0.7105 (t80) REVERT: B 1333 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8476 (ptt180) outliers start: 23 outliers final: 17 residues processed: 69 average time/residue: 0.1280 time to fit residues: 13.0765 Evaluate side-chains 67 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 37 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS B 160 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS B 754 HIS B1305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.057647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036103 restraints weight = 86326.337| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 5.94 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14448 Z= 0.291 Angle : 0.759 11.344 20106 Z= 0.356 Chirality : 0.052 0.550 2301 Planarity : 0.004 0.045 2055 Dihedral : 17.175 135.810 3098 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.75 % Allowed : 10.68 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1322 helix: 1.98 (0.21), residues: 671 sheet: -1.00 (0.53), residues: 92 loop : -0.02 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 535 TYR 0.018 0.002 TYR B1356 PHE 0.015 0.002 PHE B1204 TRP 0.046 0.003 TRP B 883 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.29 (14448) covalent geometry : angle 0.75885 / 0.36 (20106) hydrogen bonds : bond 0.04302 / 2.21 ( 641) hydrogen bonds : angle 4.50997 / 1.93 ( 1721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.9036 (mtp) cc_final: 0.8192 (mmm) REVERT: B 296 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9363 (mm) REVERT: B 383 MET cc_start: 0.8953 (tpp) cc_final: 0.8436 (tpp) REVERT: B 534 MET cc_start: 0.6929 (ppp) cc_final: 0.6703 (ppp) REVERT: B 564 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9372 (pp) REVERT: B 631 MET cc_start: 0.9185 (mmm) cc_final: 0.8797 (mtp) REVERT: B 656 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7159 (p90) REVERT: B 933 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9131 (tm-30) REVERT: B 1037 PHE cc_start: 0.7503 (t80) cc_final: 0.7156 (t80) REVERT: B 1333 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8519 (ptt180) outliers start: 21 outliers final: 13 residues processed: 65 average time/residue: 0.1173 time to fit residues: 11.4323 Evaluate side-chains 63 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 2 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.058586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037112 restraints weight = 83483.993| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 5.86 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14448 Z= 0.178 Angle : 0.662 12.254 20106 Z= 0.313 Chirality : 0.050 0.530 2301 Planarity : 0.003 0.044 2055 Dihedral : 17.085 135.101 3098 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.34 % Allowed : 11.10 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1322 helix: 2.15 (0.21), residues: 664 sheet: -0.75 (0.53), residues: 97 loop : 0.02 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 780 TYR 0.013 0.001 TYR B 5 PHE 0.012 0.001 PHE B 970 TRP 0.046 0.002 TRP B 883 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (14448) covalent geometry : angle 0.66158 / 0.31 (20106) hydrogen bonds : bond 0.03674 / 1.90 ( 641) hydrogen bonds : angle 4.33430 / 1.85 ( 1721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.40 seconds wall clock time: 50 minutes 35.57 seconds (3035.57 seconds total)