Starting phenix.real_space_refine on Sat Jul 4 01:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4c_14493/07_2026/7z4c_14493.map" } resolution = 3.87 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= 0.002 sd= 0.021 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 3714 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 145 5.49 5 S 23 5.16 5 C 8486 2.51 5 N 2483 2.21 5 O 3043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14180 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 589 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1910 Classifications: {'DNA': 1, 'RNA': 89} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 76} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 11089 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 35, 'TRANS': 1321} Chain breaks: 1 Time building chain proxies: 2.66, per 1000 atoms: 0.19 Number of scatterers: 14180 At special positions: 0 Unit cell: (92.3, 124.15, 124.8, 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 145 15.00 O 3043 8.00 N 2483 7.00 C 8486 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: 1.22 Conformation dependent library (CDL) restraints added in 490.3 milliseconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 54.4% alpha, 8.1% beta 51 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... 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 107 through 111 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.763A pdb=" N PHE B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.759A pdb=" N ASP B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.905A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.715A pdb=" N SER B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.522A 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 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.900A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.351A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.603A 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 removed outlier: 3.779A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.899A pdb=" N THR B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 525 removed outlier: 3.554A pdb=" N GLU B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.657A 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 625 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 643 removed outlier: 4.529A pdb=" N HIS B 641 " --> pdb=" O THR B 638 " (cutoff:3.500A) 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: 4.276A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 removed outlier: 3.705A pdb=" N GLN B 807 " --> pdb=" O THR B 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 807' Processing helix chain 'B' and resid 808 through 817 removed outlier: 3.642A pdb=" N TYR B 812 " --> pdb=" O ASN B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.538A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 3.555A pdb=" N VAL B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.709A 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 901 through 906 Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 4.206A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 970 " --> pdb=" O PHE B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.530A 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 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 3.513A pdb=" N TYR B1131 " --> pdb=" O ASP B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.582A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1278 removed outlier: 3.616A pdb=" N SER B1274 " --> pdb=" O ILE B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1306 through 1311 removed outlier: 3.976A pdb=" N HIS B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.592A pdb=" N LEU B1315 " --> pdb=" O LEU B1312 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B1317 " --> pdb=" O THR B1314 " (cutoff:3.500A) 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 957 removed outlier: 4.152A pdb=" N ASN B 758 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.821A pdb=" N LEU B 35 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B1359 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.759A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 removed outlier: 3.874A pdb=" N ASP B 837 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B 858 " --> pdb=" O ASP B 837 " (cutoff:3.500A) 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 1106 through 1111 removed outlier: 6.866A pdb=" N LYS B1107 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B1133 " --> pdb=" O LEU B1111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.730A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.682A 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 512 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 1.60 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: 3110 1.33 - 1.45: 3728 1.45 - 1.57: 7575 1.57 - 1.69: 290 1.69 - 1.81: 44 Bond restraints: 14747 Sorted by residual: bond pdb=" C1' DC C 5 " pdb=" N1 DC C 5 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DC C 2 " pdb=" C2' DC C 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" C1' DT D -6 " pdb=" N1 DT D -6 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.60e+00 bond pdb=" C3' DG C -6 " pdb=" C2' DG C -6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.41e+00 ... (remaining 14742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 19781 1.18 - 2.36: 614 2.36 - 3.54: 128 3.54 - 4.72: 7 4.72 - 5.90: 6 Bond angle restraints: 20536 Sorted by residual: angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O PHE B 446 " pdb=" C PHE B 446 " pdb=" N ARG B 447 " ideal model delta sigma weight residual 122.96 128.75 -5.79 1.26e+00 6.30e-01 2.11e+01 angle pdb=" N3 DT D -15 " pdb=" C4 DT D -15 " pdb=" O4 DT D -15 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT D -17 " pdb=" C4 DT D -17 " pdb=" O4 DT D -17 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 20531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8305 35.93 - 71.86: 340 71.86 - 107.78: 4 107.78 - 143.71: 1 143.71 - 179.64: 2 Dihedral angle restraints: 8652 sinusoidal: 4662 harmonic: 3990 Sorted by residual: dihedral pdb=" C4' DA D -2 " pdb=" C3' DA D -2 " pdb=" O3' DA D -2 " pdb=" P DT D -1 " ideal model delta sinusoidal sigma weight residual -140.00 39.64 -179.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' U A 80 " pdb=" C3' U A 80 " pdb=" O3' U A 80 " pdb=" P G A 81 " ideal model delta sinusoidal sigma weight residual -140.00 27.05 -167.05 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC C 5 " pdb=" C3' DC C 5 " pdb=" O3' DC C 5 " pdb=" P DT C 6 " ideal model delta sinusoidal sigma weight residual 220.00 81.09 138.91 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1689 0.035 - 0.069: 476 0.069 - 0.104: 136 0.104 - 0.138: 39 0.138 - 0.173: 2 Chirality restraints: 2342 Sorted by residual: chirality pdb=" C1' A A 12 " pdb=" O4' A A 12 " pdb=" C2' A A 12 " pdb=" N9 A A 12 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" C2' G A 16 " pdb=" C3' G A 16 " pdb=" O2' G A 16 " pdb=" C1' G A 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" C1' A A 41 " pdb=" O4' A A 41 " pdb=" C2' A A 41 " pdb=" N9 A A 41 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2339 not shown) Planarity restraints: 2093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 13 " -0.025 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" N1 U A 13 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U A 13 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U A 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U A 13 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U A 13 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 454 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PRO B 454 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 454 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 455 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 12 " -0.023 2.00e-02 2.50e+03 1.05e-02 3.06e+00 pdb=" N9 A A 12 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 12 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 12 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2090 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2437 2.77 - 3.30: 13375 3.30 - 3.83: 24711 3.83 - 4.37: 28632 4.37 - 4.90: 45023 Nonbonded interactions: 114178 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.232 3.040 nonbonded pdb=" O LEU B 551 " pdb=" OG1 THR B 555 " model vdw 2.235 3.040 nonbonded pdb=" O HIS B 799 " pdb=" OH TYR B 815 " model vdw 2.245 3.040 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLU B1357 " pdb=" NH1 ARG B1359 " model vdw 2.265 3.120 ... (remaining 114173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.410 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.047 14747 Z= 0.239 Angle : 0.498 5.903 20536 Z= 0.358 Chirality : 0.037 0.173 2342 Planarity : 0.003 0.031 2093 Dihedral : 15.464 179.639 6072 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.06 % Allowed : 4.28 % Favored : 93.67 % 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: 1.06 (0.23), residues: 1353 helix: 1.93 (0.21), residues: 656 sheet: -0.18 (0.48), residues: 118 loop : -0.52 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.011 0.001 TYR B 155 PHE 0.009 0.001 PHE B1276 TRP 0.009 0.001 TRP B 464 HIS 0.003 0.001 HIS B1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.24 (14747) covalent geometry : angle 0.49812 / 0.36 (20536) hydrogen bonds : bond 0.15410 / 17.83 ( 637) hydrogen bonds : angle 5.43938 / 7.40 ( 1709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.471 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 174 LEU cc_start: 0.9221 (pp) cc_final: 0.8865 (tp) REVERT: B 534 MET cc_start: 0.6025 (mtp) cc_final: 0.5743 (ptp) REVERT: B 703 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 727 LEU cc_start: 0.8780 (mt) cc_final: 0.8235 (mt) REVERT: B 734 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9087 (mtmt) REVERT: B 782 LYS cc_start: 0.9800 (ttmt) cc_final: 0.9568 (ptmm) REVERT: B 815 TYR cc_start: 0.9516 (m-80) cc_final: 0.8945 (m-80) REVERT: B 1004 LEU cc_start: 0.8927 (mt) cc_final: 0.8512 (mt) REVERT: B 1099 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 1333 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8684 (ptt180) outliers start: 25 outliers final: 6 residues processed: 156 average time/residue: 0.1268 time to fit residues: 28.5456 Evaluate side-chains 83 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS B 415 HIS B 612 ASN B 698 HIS ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN B 885 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN B1305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.050653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036016 restraints weight = 107214.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037350 restraints weight = 52858.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038073 restraints weight = 34570.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038576 restraints weight = 27262.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.038863 restraints weight = 23641.881| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14747 Z= 0.236 Angle : 0.622 9.618 20536 Z= 0.328 Chirality : 0.038 0.185 2342 Planarity : 0.004 0.030 2093 Dihedral : 18.137 175.516 3203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 9.46 % Favored : 88.57 % 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: 1.09 (0.23), residues: 1353 helix: 2.00 (0.21), residues: 659 sheet: 0.05 (0.54), residues: 87 loop : -0.60 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 832 TYR 0.035 0.002 TYR B 823 PHE 0.012 0.001 PHE B 375 TRP 0.009 0.002 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 (14747) covalent geometry : angle 0.62224 / 0.33 (20536) hydrogen bonds : bond 0.05411 / 5.97 ( 637) hydrogen bonds : angle 4.69567 / 6.27 ( 1709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.375 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 174 LEU cc_start: 0.9202 (pp) cc_final: 0.8729 (tp) REVERT: B 383 MET cc_start: 0.8484 (mmp) cc_final: 0.8262 (mmt) REVERT: B 534 MET cc_start: 0.6353 (mtp) cc_final: 0.5894 (ptp) REVERT: B 703 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9001 (p) REVERT: B 727 LEU cc_start: 0.8616 (mt) cc_final: 0.8210 (mt) REVERT: B 815 TYR cc_start: 0.9547 (m-80) cc_final: 0.8996 (m-80) REVERT: B 1099 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 1169 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8721 (tpt) REVERT: B 1333 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8378 (ptt180) outliers start: 24 outliers final: 14 residues processed: 90 average time/residue: 0.1151 time to fit residues: 15.6260 Evaluate side-chains 77 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 826 GLN ** B 990 ASN ** 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 = 0.3366 r_free = 0.3366 target = 0.050213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035660 restraints weight = 107679.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036974 restraints weight = 52631.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.037687 restraints weight = 34368.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038212 restraints weight = 27128.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.038455 restraints weight = 23429.512| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14747 Z= 0.180 Angle : 0.543 8.773 20536 Z= 0.289 Chirality : 0.037 0.206 2342 Planarity : 0.003 0.031 2093 Dihedral : 18.172 174.757 3203 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.81 % Allowed : 11.18 % Favored : 87.01 % 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: 1.10 (0.23), residues: 1353 helix: 2.01 (0.21), residues: 664 sheet: 0.26 (0.54), residues: 95 loop : -0.67 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.013 0.001 TYR B 823 PHE 0.010 0.001 PHE B 518 TRP 0.016 0.002 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (14747) covalent geometry : angle 0.54281 / 0.29 (20536) hydrogen bonds : bond 0.04582 / 5.00 ( 637) hydrogen bonds : angle 4.46052 / 5.92 ( 1709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.348 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 174 LEU cc_start: 0.9143 (pp) cc_final: 0.8607 (tp) REVERT: B 534 MET cc_start: 0.6501 (mtp) cc_final: 0.6024 (ptp) REVERT: B 703 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8996 (p) REVERT: B 727 LEU cc_start: 0.8657 (mt) cc_final: 0.8142 (mt) REVERT: B 751 MET cc_start: 0.9109 (tpp) cc_final: 0.8629 (ttm) REVERT: B 815 TYR cc_start: 0.9530 (m-80) cc_final: 0.8984 (m-80) REVERT: B 1021 MET cc_start: 0.8735 (mpp) cc_final: 0.8240 (tpp) REVERT: B 1093 ASN cc_start: 0.8537 (m-40) cc_final: 0.7878 (m-40) REVERT: B 1099 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 1169 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 1333 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8295 (ptt180) REVERT: B 1350 GLN cc_start: 0.8934 (mt0) cc_final: 0.8713 (tt0) outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 0.1092 time to fit residues: 13.7073 Evaluate side-chains 77 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.048751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034333 restraints weight = 110059.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035594 restraints weight = 54058.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036329 restraints weight = 35478.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036757 restraints weight = 27836.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.037024 restraints weight = 24410.599| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14747 Z= 0.238 Angle : 0.583 9.700 20536 Z= 0.312 Chirality : 0.037 0.259 2342 Planarity : 0.004 0.043 2093 Dihedral : 18.263 174.359 3203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.55 % Allowed : 11.35 % Favored : 86.10 % 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: 0.94 (0.23), residues: 1353 helix: 1.84 (0.21), residues: 673 sheet: 0.53 (0.57), residues: 88 loop : -0.81 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 864 TYR 0.013 0.001 TYR B1141 PHE 0.012 0.001 PHE B 375 TRP 0.010 0.002 TRP B 659 HIS 0.007 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.24 (14747) covalent geometry : angle 0.58260 / 0.31 (20536) hydrogen bonds : bond 0.05216 / 5.73 ( 637) hydrogen bonds : angle 4.51202 / 6.04 ( 1709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9500 (mmm) cc_final: 0.9118 (mmm) REVERT: B 703 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9011 (p) REVERT: B 727 LEU cc_start: 0.8595 (mt) cc_final: 0.8119 (mt) REVERT: B 813 LEU cc_start: 0.9830 (mt) cc_final: 0.9581 (tp) REVERT: B 815 TYR cc_start: 0.9548 (m-80) cc_final: 0.9030 (m-80) REVERT: B 822 MET cc_start: 0.8937 (mmp) cc_final: 0.8714 (mmp) REVERT: B 1021 MET cc_start: 0.8760 (mpp) cc_final: 0.8264 (tpp) REVERT: B 1099 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 1169 MET cc_start: 0.8951 (mtp) cc_final: 0.8327 (mmm) REVERT: B 1333 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: B 1350 GLN cc_start: 0.8961 (mt0) cc_final: 0.8664 (tt0) outliers start: 31 outliers final: 20 residues processed: 86 average time/residue: 0.1224 time to fit residues: 16.0536 Evaluate side-chains 75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 983 HIS ** B 990 ASN ** 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 = 0.3347 r_free = 0.3347 target = 0.049313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034800 restraints weight = 109554.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.036088 restraints weight = 53355.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036809 restraints weight = 35008.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037296 restraints weight = 27583.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037550 restraints weight = 23933.501| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14747 Z= 0.150 Angle : 0.538 11.608 20536 Z= 0.285 Chirality : 0.037 0.344 2342 Planarity : 0.003 0.045 2093 Dihedral : 18.215 174.000 3201 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.55 % Allowed : 11.76 % Favored : 85.69 % 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: 1.00 (0.23), residues: 1353 helix: 1.86 (0.21), residues: 671 sheet: 0.56 (0.56), residues: 88 loop : -0.72 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.032 0.001 TYR B 823 PHE 0.008 0.001 PHE B 846 TRP 0.008 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14747) covalent geometry : angle 0.53794 / 0.28 (20536) hydrogen bonds : bond 0.04180 / 4.55 ( 637) hydrogen bonds : angle 4.31066 / 5.77 ( 1709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9510 (mmm) cc_final: 0.9132 (mmm) REVERT: B 103 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8438 (pp20) REVERT: B 383 MET cc_start: 0.8540 (mmp) cc_final: 0.8111 (mmt) REVERT: B 534 MET cc_start: 0.6129 (ttm) cc_final: 0.4756 (ptm) REVERT: B 703 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 727 LEU cc_start: 0.8625 (mt) cc_final: 0.8048 (mt) REVERT: B 751 MET cc_start: 0.9139 (tpp) cc_final: 0.8627 (tpp) REVERT: B 801 VAL cc_start: 0.5241 (OUTLIER) cc_final: 0.4505 (p) REVERT: B 815 TYR cc_start: 0.9546 (m-80) cc_final: 0.9045 (m-80) REVERT: B 1021 MET cc_start: 0.8762 (mpp) cc_final: 0.8315 (mmp) REVERT: B 1099 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 1169 MET cc_start: 0.8917 (mtp) cc_final: 0.8240 (mmm) REVERT: B 1333 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8346 (ptt180) REVERT: B 1350 GLN cc_start: 0.8929 (mt0) cc_final: 0.8648 (tt0) REVERT: B 1357 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8397 (mp0) outliers start: 31 outliers final: 20 residues processed: 81 average time/residue: 0.1235 time to fit residues: 15.1030 Evaluate side-chains 78 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 20.0000 chunk 133 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.049588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.035125 restraints weight = 108142.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036424 restraints weight = 52390.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037127 restraints weight = 34202.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037625 restraints weight = 27080.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037854 restraints weight = 23477.229| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14747 Z= 0.124 Angle : 0.524 9.907 20536 Z= 0.276 Chirality : 0.036 0.217 2342 Planarity : 0.003 0.048 2093 Dihedral : 18.173 173.887 3201 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.14 % Allowed : 12.83 % Favored : 85.03 % 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: 1.02 (0.23), residues: 1353 helix: 1.84 (0.21), residues: 676 sheet: 0.51 (0.56), residues: 88 loop : -0.67 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 654 TYR 0.015 0.001 TYR B 823 PHE 0.007 0.001 PHE B 846 TRP 0.006 0.001 TRP B 18 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14747) covalent geometry : angle 0.52395 / 0.28 (20536) hydrogen bonds : bond 0.03839 / 4.19 ( 637) hydrogen bonds : angle 4.17781 / 5.62 ( 1709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8405 (pp20) REVERT: B 174 LEU cc_start: 0.9195 (pp) cc_final: 0.8696 (tp) REVERT: B 383 MET cc_start: 0.8538 (mmp) cc_final: 0.8115 (mmt) REVERT: B 534 MET cc_start: 0.6122 (ttm) cc_final: 0.4820 (ptm) REVERT: B 703 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 727 LEU cc_start: 0.8600 (mt) cc_final: 0.7917 (mt) REVERT: B 801 VAL cc_start: 0.4974 (OUTLIER) cc_final: 0.4252 (p) REVERT: B 815 TYR cc_start: 0.9511 (m-80) cc_final: 0.9027 (m-80) REVERT: B 1021 MET cc_start: 0.8763 (mpp) cc_final: 0.8295 (mmp) REVERT: B 1099 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 1169 MET cc_start: 0.8922 (mtp) cc_final: 0.8301 (mmm) REVERT: B 1219 GLU cc_start: 0.8026 (tt0) cc_final: 0.7767 (mt-10) REVERT: B 1333 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8369 (ptt180) REVERT: B 1350 GLN cc_start: 0.8909 (mt0) cc_final: 0.8636 (tt0) REVERT: B 1357 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8415 (mp0) outliers start: 26 outliers final: 18 residues processed: 81 average time/residue: 0.1120 time to fit residues: 13.8566 Evaluate side-chains 75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 0.0070 chunk 137 optimal weight: 7.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.049540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035154 restraints weight = 107325.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036422 restraints weight = 52041.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037196 restraints weight = 34386.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037622 restraints weight = 26707.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037911 restraints weight = 23348.676| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14747 Z= 0.124 Angle : 0.526 11.949 20536 Z= 0.276 Chirality : 0.036 0.240 2342 Planarity : 0.003 0.042 2093 Dihedral : 18.146 173.861 3201 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.38 % Allowed : 13.08 % Favored : 84.54 % 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: 1.07 (0.23), residues: 1353 helix: 1.86 (0.21), residues: 677 sheet: 0.53 (0.56), residues: 88 loop : -0.63 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 654 TYR 0.008 0.001 TYR B 988 PHE 0.007 0.001 PHE B 846 TRP 0.005 0.001 TRP B 18 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14747) covalent geometry : angle 0.52638 / 0.28 (20536) hydrogen bonds : bond 0.03803 / 4.14 ( 637) hydrogen bonds : angle 4.12754 / 5.55 ( 1709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9530 (mmm) cc_final: 0.9212 (mmm) REVERT: B 103 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: B 174 LEU cc_start: 0.9181 (pp) cc_final: 0.8707 (tp) REVERT: B 383 MET cc_start: 0.8565 (mmp) cc_final: 0.7976 (mmp) REVERT: B 534 MET cc_start: 0.6086 (ttm) cc_final: 0.4842 (ptm) REVERT: B 703 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8816 (t) REVERT: B 727 LEU cc_start: 0.8601 (mt) cc_final: 0.7916 (mt) REVERT: B 751 MET cc_start: 0.9076 (tpp) cc_final: 0.8568 (tpp) REVERT: B 801 VAL cc_start: 0.5082 (OUTLIER) cc_final: 0.4435 (p) REVERT: B 813 LEU cc_start: 0.9825 (mt) cc_final: 0.9596 (tp) REVERT: B 815 TYR cc_start: 0.9500 (m-80) cc_final: 0.9040 (m-80) REVERT: B 1021 MET cc_start: 0.8770 (mpp) cc_final: 0.8288 (mmp) REVERT: B 1099 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8045 (mt-10) REVERT: B 1169 MET cc_start: 0.8914 (mtp) cc_final: 0.8313 (mmm) REVERT: B 1219 GLU cc_start: 0.7927 (tt0) cc_final: 0.7669 (mt-10) REVERT: B 1333 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8303 (ptt180) REVERT: B 1357 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8425 (mp0) outliers start: 29 outliers final: 18 residues processed: 83 average time/residue: 0.1034 time to fit residues: 13.2720 Evaluate side-chains 76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.048220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033938 restraints weight = 109922.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035194 restraints weight = 53886.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035887 restraints weight = 35420.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.036354 restraints weight = 27938.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036526 restraints weight = 24271.181| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14747 Z= 0.212 Angle : 0.590 13.235 20536 Z= 0.310 Chirality : 0.037 0.223 2342 Planarity : 0.003 0.041 2093 Dihedral : 18.240 174.132 3201 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.23), residues: 1353 helix: 1.83 (0.21), residues: 671 sheet: 0.59 (0.58), residues: 88 loop : -0.58 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.012 0.001 TYR B1013 PHE 0.010 0.001 PHE B 375 TRP 0.009 0.002 TRP B 659 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (14747) covalent geometry : angle 0.59026 / 0.31 (20536) hydrogen bonds : bond 0.04741 / 5.20 ( 637) hydrogen bonds : angle 4.29969 / 5.81 ( 1709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9551 (mmm) cc_final: 0.9129 (mmm) REVERT: B 383 MET cc_start: 0.8590 (mmp) cc_final: 0.7994 (mmp) REVERT: B 534 MET cc_start: 0.6114 (ttm) cc_final: 0.4932 (ptm) REVERT: B 727 LEU cc_start: 0.8654 (mt) cc_final: 0.7991 (mt) REVERT: B 751 MET cc_start: 0.9127 (tpp) cc_final: 0.8597 (tpp) REVERT: B 801 VAL cc_start: 0.5233 (OUTLIER) cc_final: 0.4578 (p) REVERT: B 813 LEU cc_start: 0.9838 (mt) cc_final: 0.9623 (tp) REVERT: B 815 TYR cc_start: 0.9532 (m-80) cc_final: 0.9065 (m-80) REVERT: B 1021 MET cc_start: 0.8788 (mpp) cc_final: 0.8312 (mmp) REVERT: B 1099 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8147 (mt-10) REVERT: B 1169 MET cc_start: 0.8904 (mtp) cc_final: 0.8205 (mmm) REVERT: B 1219 GLU cc_start: 0.7953 (tt0) cc_final: 0.7713 (mt-10) REVERT: B 1333 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8304 (ptt180) outliers start: 24 outliers final: 20 residues processed: 74 average time/residue: 0.1119 time to fit residues: 13.0828 Evaluate side-chains 74 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 3 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.048165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033925 restraints weight = 110986.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.035168 restraints weight = 54241.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.035931 restraints weight = 35661.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036321 restraints weight = 27760.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036614 restraints weight = 24424.046| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14747 Z= 0.194 Angle : 0.587 13.647 20536 Z= 0.308 Chirality : 0.037 0.198 2342 Planarity : 0.003 0.041 2093 Dihedral : 18.278 174.043 3201 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.81 % Allowed : 14.14 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1353 helix: 1.77 (0.21), residues: 671 sheet: 0.54 (0.57), residues: 88 loop : -0.60 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.011 0.001 TYR B1013 PHE 0.008 0.001 PHE B 846 TRP 0.009 0.002 TRP B 18 HIS 0.007 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (14747) covalent geometry : angle 0.58733 / 0.31 (20536) hydrogen bonds : bond 0.04319 / 4.74 ( 637) hydrogen bonds : angle 4.27401 / 5.77 ( 1709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.613 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: B 90 MET cc_start: 0.9539 (mmm) cc_final: 0.9235 (mmm) REVERT: B 383 MET cc_start: 0.8581 (mmp) cc_final: 0.7968 (mmp) REVERT: B 534 MET cc_start: 0.6124 (ttm) cc_final: 0.4970 (ptm) REVERT: B 727 LEU cc_start: 0.8668 (mt) cc_final: 0.8020 (mt) REVERT: B 801 VAL cc_start: 0.5398 (OUTLIER) cc_final: 0.4805 (p) REVERT: B 813 LEU cc_start: 0.9838 (mt) cc_final: 0.9622 (tp) REVERT: B 815 TYR cc_start: 0.9531 (m-80) cc_final: 0.9062 (m-80) REVERT: B 1021 MET cc_start: 0.8818 (mpp) cc_final: 0.8270 (tpp) REVERT: B 1099 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 1169 MET cc_start: 0.8891 (mtp) cc_final: 0.8196 (mmm) REVERT: B 1219 GLU cc_start: 0.7892 (tt0) cc_final: 0.7630 (mt-10) REVERT: B 1333 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8321 (ptt180) outliers start: 22 outliers final: 18 residues processed: 74 average time/residue: 0.1208 time to fit residues: 13.7603 Evaluate side-chains 75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 88 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 1.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.034640 restraints weight = 109270.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035931 restraints weight = 53423.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036657 restraints weight = 34971.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037153 restraints weight = 27515.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037392 restraints weight = 23717.312| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14747 Z= 0.113 Angle : 0.554 12.677 20536 Z= 0.287 Chirality : 0.037 0.194 2342 Planarity : 0.003 0.041 2093 Dihedral : 18.182 174.029 3201 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.73 % Allowed : 14.31 % Favored : 83.96 % 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: 1.15 (0.23), residues: 1353 helix: 1.87 (0.21), residues: 672 sheet: 0.57 (0.56), residues: 88 loop : -0.48 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 780 TYR 0.013 0.001 TYR B1013 PHE 0.007 0.001 PHE B 518 TRP 0.006 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (14747) covalent geometry : angle 0.55427 / 0.29 (20536) hydrogen bonds : bond 0.03563 / 3.87 ( 637) hydrogen bonds : angle 4.06337 / 5.51 ( 1709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9529 (mmm) cc_final: 0.9215 (mmm) REVERT: B 103 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8317 (pp20) REVERT: B 174 LEU cc_start: 0.9184 (pp) cc_final: 0.8770 (tp) REVERT: B 534 MET cc_start: 0.6095 (ttm) cc_final: 0.4907 (ptm) REVERT: B 727 LEU cc_start: 0.8657 (mt) cc_final: 0.8143 (mt) REVERT: B 751 MET cc_start: 0.9043 (tpp) cc_final: 0.8583 (ttm) REVERT: B 801 VAL cc_start: 0.5413 (OUTLIER) cc_final: 0.4684 (p) REVERT: B 813 LEU cc_start: 0.9838 (mt) cc_final: 0.9624 (tp) REVERT: B 815 TYR cc_start: 0.9487 (m-80) cc_final: 0.9029 (m-80) REVERT: B 1021 MET cc_start: 0.8751 (mpp) cc_final: 0.8245 (mpp) REVERT: B 1099 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 1169 MET cc_start: 0.8937 (mtp) cc_final: 0.8335 (mmm) REVERT: B 1219 GLU cc_start: 0.7767 (tt0) cc_final: 0.7031 (mt-10) REVERT: B 1333 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8308 (ptt180) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.1102 time to fit residues: 13.5557 Evaluate side-chains 72 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 102 optimal weight: 0.0050 chunk 106 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 2.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034502 restraints weight = 109482.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.035736 restraints weight = 52863.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036499 restraints weight = 34813.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.036956 restraints weight = 27162.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037196 restraints weight = 23633.077| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14747 Z= 0.150 Angle : 0.562 12.458 20536 Z= 0.294 Chirality : 0.036 0.188 2342 Planarity : 0.003 0.041 2093 Dihedral : 18.191 174.249 3200 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.56 % Allowed : 14.56 % Favored : 83.88 % 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: 1.22 (0.23), residues: 1353 helix: 1.91 (0.21), residues: 672 sheet: 0.65 (0.57), residues: 88 loop : -0.43 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.011 0.001 TYR B1013 PHE 0.008 0.001 PHE B 846 TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (14747) covalent geometry : angle 0.56229 / 0.29 (20536) hydrogen bonds : bond 0.03920 / 4.26 ( 637) hydrogen bonds : angle 4.10705 / 5.54 ( 1709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.39 seconds wall clock time: 42 minutes 18.75 seconds (2538.75 seconds total)