Starting phenix.real_space_refine on Wed Aug 5 03:11:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg4_45568/08_2026/9cg4_45568.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 52 5.16 5 C 5146 2.51 5 N 1391 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8375 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1468 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "A" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 2.13, per 1000 atoms: 0.25 Number of scatterers: 8375 At special positions: 0 Unit cell: (97.734, 109.548, 128.88, 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 52 16.00 P 43 15.00 O 1743 8.00 N 1391 7.00 C 5146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 345.2 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 32.1% alpha, 20.1% beta 14 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 removed outlier: 4.179A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.565A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.844A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.871A pdb=" N GLU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 261' Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.299A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.602A pdb=" N CYS C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.917A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.532A pdb=" N SER C 261 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 removed outlier: 4.226A pdb=" N LEU D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.779A pdb=" N CYS D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing helix chain 'E' and resid 373 through 389 removed outlier: 3.685A pdb=" N ARG E 377 " --> pdb=" O PRO E 373 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 378 " --> pdb=" O TYR E 374 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 382 " --> pdb=" O SER E 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 383 " --> pdb=" O PHE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 removed outlier: 3.528A pdb=" N LEU E 395 " --> pdb=" O ASP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 410 removed outlier: 4.017A pdb=" N VAL E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 424 removed outlier: 3.573A pdb=" N TYR E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 443 through 453 removed outlier: 3.587A pdb=" N ALA E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 464 through 472 Processing helix chain 'E' and resid 473 through 484 Processing helix chain 'E' and resid 492 through 504 Processing helix chain 'E' and resid 509 through 513 Processing helix chain 'E' and resid 518 through 532 removed outlier: 3.906A pdb=" N VAL E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 546 Processing helix chain 'E' and resid 548 through 554 removed outlier: 3.592A pdb=" N SER E 553 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.796A pdb=" N ILE B 30 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 70 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 26 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS B 246 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.635A pdb=" N ASN C 177 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.503A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.801A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.938A pdb=" N VAL C 48 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AB4, first strand: chain 'D' and resid 66 through 71 removed outlier: 3.712A pdb=" N MET D 68 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 70 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 26 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU D 25 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET D 40 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 48 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER D 230 " --> pdb=" O PRO D 234 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 429 through 430 299 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 1990 1.46 - 1.58: 3811 1.58 - 1.71: 84 1.71 - 1.83: 84 Bond restraints: 8584 Sorted by residual: bond pdb=" C3' DC F 23 " pdb=" C2' DC F 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DT F 22 " pdb=" C2' DT F 22 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.20e+00 bond pdb=" C3' DG F 26 " pdb=" C2' DG F 26 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.70e+00 bond pdb=" C3' DC F 25 " pdb=" C2' DC F 25 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.67e+00 bond pdb=" C3' DT F 24 " pdb=" C2' DT F 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.46e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11494 1.92 - 3.84: 238 3.84 - 5.76: 32 5.76 - 7.69: 8 7.69 - 9.61: 5 Bond angle restraints: 11777 Sorted by residual: angle pdb=" CA GLN C 108 " pdb=" CB GLN C 108 " pdb=" CG GLN C 108 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.83e+01 angle pdb=" N3 DT A 6 " pdb=" C4 DT A 6 " pdb=" O4 DT A 6 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT F 31 " pdb=" C4 DT F 31 " pdb=" O4 DT F 31 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT F 38 " pdb=" C4 DT F 38 " pdb=" O4 DT F 38 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT F 37 " pdb=" C4 DT F 37 " pdb=" O4 DT F 37 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 11772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 4799 32.67 - 65.34: 358 65.34 - 98.01: 13 98.01 - 130.68: 0 130.68 - 163.35: 2 Dihedral angle restraints: 5172 sinusoidal: 2354 harmonic: 2818 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual -86.00 -122.16 36.16 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 162 " pdb=" CB CYS D 162 " ideal model delta sinusoidal sigma weight residual -86.00 -119.20 33.20 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" C4' DG F 26 " pdb=" C3' DG F 26 " pdb=" O3' DG F 26 " pdb=" P DA F 27 " ideal model delta sinusoidal sigma weight residual 220.00 56.65 163.35 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 5169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 892 0.035 - 0.071: 324 0.071 - 0.106: 123 0.106 - 0.141: 34 0.141 - 0.177: 4 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA GLN C 108 " pdb=" N GLN C 108 " pdb=" C GLN C 108 " pdb=" CB GLN C 108 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA ASP B 232 " pdb=" N ASP B 232 " pdb=" C ASP B 232 " pdb=" CB ASP B 232 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA THR E 444 " pdb=" N THR E 444 " pdb=" C THR E 444 " pdb=" CB THR E 444 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 1374 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 89 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C THR D 89 " 0.037 2.00e-02 2.50e+03 pdb=" O THR D 89 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU D 90 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 102 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C VAL D 102 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL D 102 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE D 103 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 243 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" CG ASP B 243 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP B 243 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP B 243 " 0.009 2.00e-02 2.50e+03 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1434 2.77 - 3.30: 7972 3.30 - 3.83: 13408 3.83 - 4.37: 15116 4.37 - 4.90: 25556 Nonbonded interactions: 63486 Sorted by model distance: nonbonded pdb=" OG SER C 152 " pdb=" OD1 ASN C 213 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP D 41 " pdb=" OG SER D 43 " model vdw 2.264 3.040 nonbonded pdb=" N GLU E 437 " pdb=" OE1 GLU E 437 " model vdw 2.265 3.120 nonbonded pdb=" N ASP E 397 " pdb=" OE1 GLU E 400 " model vdw 2.275 3.120 nonbonded pdb=" O ILE E 447 " pdb=" OG1 THR E 451 " model vdw 2.279 3.040 ... (remaining 63481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.004 0.040 8587 Z= 0.257 Angle : 0.649 9.606 11783 Z= 0.410 Chirality : 0.044 0.177 1377 Planarity : 0.003 0.026 1358 Dihedral : 19.709 163.352 3333 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.35 % Allowed : 29.79 % Favored : 69.86 % 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: -0.68 (0.28), residues: 958 helix: 1.77 (0.34), residues: 232 sheet: -1.39 (0.28), residues: 359 loop : -0.73 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 146 TYR 0.016 0.001 TYR B 249 PHE 0.011 0.001 PHE B 169 TRP 0.002 0.001 TRP C 28 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.26 ( 8584) covalent geometry : angle 0.64857 / 0.41 (11777) SS BOND : bond 0.00463 / 0.24 ( 3) SS BOND : angle 1.58153 / 0.79 ( 6) hydrogen bonds : bond 0.27926 / 18.64 ( 331) hydrogen bonds : angle 7.92649 / 5.77 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1075 time to fit residues: 15.6880 Evaluate side-chains 97 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 ASN D 213 ASN E 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.093389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058696 restraints weight = 22461.263| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.55 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8587 Z= 0.153 Angle : 0.629 10.733 11783 Z= 0.340 Chirality : 0.044 0.234 1377 Planarity : 0.003 0.031 1358 Dihedral : 19.540 166.418 1498 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.13 % Allowed : 26.12 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 958 helix: 1.59 (0.34), residues: 243 sheet: -1.03 (0.29), residues: 357 loop : -0.88 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.024 0.002 TYR E 408 PHE 0.011 0.001 PHE B 169 TRP 0.003 0.001 TRP C 28 HIS 0.006 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 8584) covalent geometry : angle 0.62798 / 0.34 (11777) SS BOND : bond 0.00527 / 0.27 ( 3) SS BOND : angle 1.45391 / 0.72 ( 6) hydrogen bonds : bond 0.07765 / 4.93 ( 331) hydrogen bonds : angle 5.28570 / 3.82 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8314 (mp10) cc_final: 0.8008 (mp10) REVERT: B 232 ASP cc_start: 0.8648 (t0) cc_final: 0.8433 (p0) REVERT: C 41 ASP cc_start: 0.8089 (t0) cc_final: 0.7663 (t0) REVERT: E 377 ARG cc_start: 0.9112 (mpp80) cc_final: 0.8887 (mpp80) REVERT: E 420 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7680 (mmt90) REVERT: E 431 MET cc_start: 0.8827 (tpp) cc_final: 0.8342 (tpp) REVERT: E 490 ASN cc_start: 0.9374 (p0) cc_final: 0.9064 (m110) outliers start: 18 outliers final: 9 residues processed: 116 average time/residue: 0.0965 time to fit residues: 14.8264 Evaluate side-chains 103 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 409 GLN E 463 GLN E 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.094081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059487 restraints weight = 22757.465| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.48 r_work: 0.2792 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8587 Z= 0.174 Angle : 0.609 10.371 11783 Z= 0.325 Chirality : 0.043 0.240 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.551 167.002 1496 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.66 % Allowed : 24.94 % Favored : 71.39 % 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: -0.46 (0.28), residues: 958 helix: 1.66 (0.34), residues: 248 sheet: -1.04 (0.29), residues: 353 loop : -0.77 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.045 0.002 TYR E 408 PHE 0.019 0.001 PHE E 407 TRP 0.015 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 8584) covalent geometry : angle 0.60841 / 0.33 (11777) SS BOND : bond 0.00510 / 0.27 ( 3) SS BOND : angle 1.15898 / 0.59 ( 6) hydrogen bonds : bond 0.06423 / 4.05 ( 331) hydrogen bonds : angle 4.84696 / 3.48 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8551 (mp10) cc_final: 0.8248 (mp10) REVERT: B 17 GLU cc_start: 0.9106 (tp30) cc_final: 0.8897 (tp30) REVERT: B 198 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: B 199 MET cc_start: 0.8649 (tpt) cc_final: 0.8266 (tpt) REVERT: B 232 ASP cc_start: 0.8725 (t0) cc_final: 0.8501 (p0) REVERT: C 41 ASP cc_start: 0.8331 (t0) cc_final: 0.7864 (t0) REVERT: D 1 MET cc_start: 0.8919 (ppp) cc_final: 0.7756 (ppp) REVERT: E 377 ARG cc_start: 0.9132 (mpp80) cc_final: 0.8804 (mpp80) REVERT: E 431 MET cc_start: 0.9047 (tpp) cc_final: 0.8268 (tpp) REVERT: E 490 ASN cc_start: 0.9385 (p0) cc_final: 0.9105 (m110) REVERT: E 545 PHE cc_start: 0.9143 (t80) cc_final: 0.8885 (t80) outliers start: 31 outliers final: 16 residues processed: 127 average time/residue: 0.0842 time to fit residues: 14.3610 Evaluate side-chains 112 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.095124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060493 restraints weight = 22970.969| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.52 r_work: 0.2822 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8587 Z= 0.117 Angle : 0.568 8.547 11783 Z= 0.304 Chirality : 0.043 0.259 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.586 167.213 1496 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 26.24 % Favored : 70.69 % 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: -0.35 (0.28), residues: 958 helix: 1.71 (0.34), residues: 248 sheet: -0.87 (0.29), residues: 351 loop : -0.79 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.008 0.001 TYR C 249 PHE 0.013 0.001 PHE E 407 TRP 0.013 0.001 TRP C 28 HIS 0.002 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 8584) covalent geometry : angle 0.56790 / 0.30 (11777) SS BOND : bond 0.00673 / 0.35 ( 3) SS BOND : angle 1.08511 / 0.55 ( 6) hydrogen bonds : bond 0.05566 / 3.44 ( 331) hydrogen bonds : angle 4.56454 / 3.28 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7616 (ppp) cc_final: 0.7324 (ppp) REVERT: B 199 MET cc_start: 0.8606 (tpt) cc_final: 0.8236 (tpt) REVERT: C 40 MET cc_start: 0.8969 (tpp) cc_final: 0.8489 (tpp) REVERT: C 41 ASP cc_start: 0.8291 (t0) cc_final: 0.8058 (t0) REVERT: C 44 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8633 (t-90) REVERT: C 61 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8055 (ttp80) REVERT: D 1 MET cc_start: 0.8969 (ppp) cc_final: 0.7918 (ppp) REVERT: D 68 MET cc_start: 0.8347 (mtm) cc_final: 0.8128 (mpp) REVERT: D 131 GLN cc_start: 0.8015 (pm20) cc_final: 0.7774 (pm20) REVERT: E 377 ARG cc_start: 0.9167 (mpp80) cc_final: 0.8819 (mpp80) REVERT: E 431 MET cc_start: 0.8969 (tpp) cc_final: 0.8309 (tpp) REVERT: E 490 ASN cc_start: 0.9348 (p0) cc_final: 0.9031 (m110) outliers start: 26 outliers final: 16 residues processed: 125 average time/residue: 0.0900 time to fit residues: 15.2289 Evaluate side-chains 114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060688 restraints weight = 22825.148| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.55 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8587 Z= 0.114 Angle : 0.562 8.083 11783 Z= 0.301 Chirality : 0.043 0.260 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.582 167.747 1496 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.02 % Allowed : 25.18 % Favored : 70.80 % 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: -0.23 (0.28), residues: 958 helix: 1.83 (0.34), residues: 248 sheet: -0.76 (0.29), residues: 349 loop : -0.79 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.010 0.001 TYR B 249 PHE 0.010 0.001 PHE E 422 TRP 0.013 0.001 TRP C 28 HIS 0.002 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8584) covalent geometry : angle 0.56185 / 0.30 (11777) SS BOND : bond 0.00550 / 0.28 ( 3) SS BOND : angle 1.15832 / 0.57 ( 6) hydrogen bonds : bond 0.05342 / 3.30 ( 331) hydrogen bonds : angle 4.41944 / 3.16 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7531 (ppp) cc_final: 0.7317 (ppp) REVERT: B 8 GLN cc_start: 0.8377 (mp10) cc_final: 0.8130 (mp10) REVERT: B 199 MET cc_start: 0.8460 (tpt) cc_final: 0.8039 (tpt) REVERT: C 61 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7704 (ttp80) REVERT: D 1 MET cc_start: 0.8989 (ppp) cc_final: 0.7936 (ppp) REVERT: D 68 MET cc_start: 0.8123 (mtm) cc_final: 0.7889 (mpp) REVERT: D 131 GLN cc_start: 0.7933 (pm20) cc_final: 0.7716 (pm20) REVERT: D 249 TYR cc_start: 0.8580 (m-80) cc_final: 0.8281 (m-10) REVERT: E 377 ARG cc_start: 0.9136 (mpp80) cc_final: 0.8792 (mpp80) REVERT: E 431 MET cc_start: 0.8945 (tpp) cc_final: 0.8284 (tpp) REVERT: E 463 GLN cc_start: 0.8701 (mm110) cc_final: 0.8481 (mm110) REVERT: E 490 ASN cc_start: 0.9336 (p0) cc_final: 0.9012 (m110) REVERT: E 506 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8335 (mp10) outliers start: 34 outliers final: 20 residues processed: 132 average time/residue: 0.0869 time to fit residues: 15.5255 Evaluate side-chains 120 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 31 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061000 restraints weight = 22387.920| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.47 r_work: 0.2845 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8587 Z= 0.107 Angle : 0.553 7.628 11783 Z= 0.296 Chirality : 0.043 0.265 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.576 168.247 1496 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.31 % Allowed : 24.82 % Favored : 71.87 % 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: -0.17 (0.28), residues: 958 helix: 1.86 (0.34), residues: 248 sheet: -0.70 (0.29), residues: 349 loop : -0.77 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.010 0.001 TYR B 249 PHE 0.014 0.001 PHE E 545 TRP 0.014 0.001 TRP C 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 8584) covalent geometry : angle 0.55313 / 0.30 (11777) SS BOND : bond 0.00570 / 0.30 ( 3) SS BOND : angle 1.02655 / 0.51 ( 6) hydrogen bonds : bond 0.05061 / 3.09 ( 331) hydrogen bonds : angle 4.26531 / 3.05 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8515 (mp10) cc_final: 0.8255 (mp10) REVERT: B 199 MET cc_start: 0.8621 (tpt) cc_final: 0.8056 (tpt) REVERT: D 1 MET cc_start: 0.9017 (ppp) cc_final: 0.7983 (ppp) REVERT: D 68 MET cc_start: 0.8188 (mtm) cc_final: 0.7919 (mpp) REVERT: D 168 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8805 (ttpp) REVERT: D 249 TYR cc_start: 0.8858 (m-80) cc_final: 0.8617 (m-10) REVERT: E 377 ARG cc_start: 0.9151 (mpp80) cc_final: 0.8777 (mpp80) REVERT: E 431 MET cc_start: 0.9068 (tpp) cc_final: 0.8398 (tpp) REVERT: E 490 ASN cc_start: 0.9332 (p0) cc_final: 0.8983 (m110) REVERT: E 506 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8426 (mp10) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.0916 time to fit residues: 15.7484 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.095459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060740 restraints weight = 22825.469| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.52 r_work: 0.2829 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8587 Z= 0.126 Angle : 0.571 7.801 11783 Z= 0.303 Chirality : 0.043 0.242 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.578 165.772 1496 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.90 % Allowed : 25.06 % Favored : 71.04 % 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: -0.13 (0.28), residues: 958 helix: 1.91 (0.34), residues: 248 sheet: -0.69 (0.29), residues: 349 loop : -0.75 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.010 0.001 TYR B 249 PHE 0.013 0.001 PHE C 2 TRP 0.013 0.001 TRP C 28 HIS 0.002 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 8584) covalent geometry : angle 0.57061 / 0.30 (11777) SS BOND : bond 0.00468 / 0.24 ( 3) SS BOND : angle 1.33999 / 0.65 ( 6) hydrogen bonds : bond 0.05007 / 3.07 ( 331) hydrogen bonds : angle 4.24563 / 3.03 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8541 (mp10) cc_final: 0.8250 (mp10) REVERT: B 199 MET cc_start: 0.8649 (tpt) cc_final: 0.8189 (tpt) REVERT: C 40 MET cc_start: 0.8897 (tpp) cc_final: 0.8440 (tpp) REVERT: C 125 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8743 (tm-30) REVERT: D 1 MET cc_start: 0.9013 (ppp) cc_final: 0.7985 (ppp) REVERT: D 68 MET cc_start: 0.8240 (mtm) cc_final: 0.7967 (mpp) REVERT: D 119 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7811 (ptp) REVERT: D 168 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8782 (ttpp) REVERT: D 249 TYR cc_start: 0.8924 (m-80) cc_final: 0.8671 (m-10) REVERT: E 377 ARG cc_start: 0.9143 (mpp80) cc_final: 0.8801 (mpp80) REVERT: E 431 MET cc_start: 0.9061 (tpp) cc_final: 0.8361 (tpp) REVERT: E 490 ASN cc_start: 0.9388 (p0) cc_final: 0.9074 (m110) REVERT: E 506 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8422 (mm-40) REVERT: E 545 PHE cc_start: 0.9091 (t80) cc_final: 0.8852 (t80) outliers start: 33 outliers final: 24 residues processed: 121 average time/residue: 0.0775 time to fit residues: 12.8442 Evaluate side-chains 122 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.094696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060778 restraints weight = 22248.011| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.37 r_work: 0.2839 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8587 Z= 0.121 Angle : 0.564 7.496 11783 Z= 0.300 Chirality : 0.043 0.223 1377 Planarity : 0.003 0.036 1358 Dihedral : 19.559 163.198 1496 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.43 % Allowed : 25.30 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.28), residues: 958 helix: 1.91 (0.34), residues: 248 sheet: -0.64 (0.29), residues: 349 loop : -0.78 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.012 0.001 TYR B 249 PHE 0.010 0.001 PHE C 2 TRP 0.014 0.001 TRP C 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8584) covalent geometry : angle 0.56331 / 0.30 (11777) SS BOND : bond 0.00483 / 0.25 ( 3) SS BOND : angle 1.32043 / 0.64 ( 6) hydrogen bonds : bond 0.04893 / 2.98 ( 331) hydrogen bonds : angle 4.18997 / 2.98 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8529 (mp10) cc_final: 0.8233 (mp10) REVERT: B 40 MET cc_start: 0.7896 (ptm) cc_final: 0.7612 (ptm) REVERT: B 199 MET cc_start: 0.8669 (tpt) cc_final: 0.8207 (tpt) REVERT: C 40 MET cc_start: 0.8862 (tpp) cc_final: 0.8413 (tpp) REVERT: C 125 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 1 MET cc_start: 0.9014 (ppp) cc_final: 0.8040 (ppp) REVERT: D 68 MET cc_start: 0.8312 (mtm) cc_final: 0.8042 (mpp) REVERT: D 119 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7826 (ptp) REVERT: D 168 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8799 (ttpp) REVERT: D 249 TYR cc_start: 0.8901 (m-80) cc_final: 0.8681 (m-10) REVERT: E 377 ARG cc_start: 0.9148 (mpp80) cc_final: 0.8837 (mpp80) REVERT: E 431 MET cc_start: 0.9128 (tpp) cc_final: 0.8626 (tpp) REVERT: E 490 ASN cc_start: 0.9368 (p0) cc_final: 0.9063 (m110) REVERT: E 545 PHE cc_start: 0.9096 (t80) cc_final: 0.8836 (t80) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.0964 time to fit residues: 16.0112 Evaluate side-chains 118 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.095292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060609 restraints weight = 22870.957| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.53 r_work: 0.2822 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8587 Z= 0.128 Angle : 0.576 7.742 11783 Z= 0.305 Chirality : 0.043 0.216 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.545 161.875 1496 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.43 % Allowed : 26.12 % Favored : 70.45 % 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: -0.09 (0.28), residues: 958 helix: 1.91 (0.34), residues: 248 sheet: -0.63 (0.29), residues: 360 loop : -0.72 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.013 0.001 TYR B 249 PHE 0.011 0.001 PHE E 422 TRP 0.011 0.001 TRP C 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8584) covalent geometry : angle 0.57553 / 0.30 (11777) SS BOND : bond 0.00476 / 0.25 ( 3) SS BOND : angle 1.29558 / 0.64 ( 6) hydrogen bonds : bond 0.04849 / 2.95 ( 331) hydrogen bonds : angle 4.17334 / 2.97 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8525 (mp10) cc_final: 0.8216 (mp10) REVERT: B 199 MET cc_start: 0.8676 (tpt) cc_final: 0.8224 (tpt) REVERT: C 125 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8740 (tm-30) REVERT: D 1 MET cc_start: 0.8997 (ppp) cc_final: 0.8019 (ppp) REVERT: D 68 MET cc_start: 0.8312 (mtm) cc_final: 0.8016 (mpp) REVERT: D 119 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7850 (ptp) REVERT: D 168 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8777 (ttpp) REVERT: D 249 TYR cc_start: 0.8942 (m-80) cc_final: 0.8724 (m-10) REVERT: E 377 ARG cc_start: 0.9150 (mpp80) cc_final: 0.8830 (mpp80) REVERT: E 431 MET cc_start: 0.9013 (tpp) cc_final: 0.8670 (tpp) REVERT: E 490 ASN cc_start: 0.9391 (p0) cc_final: 0.9099 (m110) REVERT: E 545 PHE cc_start: 0.9136 (t80) cc_final: 0.8829 (t80) outliers start: 29 outliers final: 22 residues processed: 119 average time/residue: 0.0952 time to fit residues: 15.6450 Evaluate side-chains 117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.093930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059696 restraints weight = 22516.998| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.46 r_work: 0.2815 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8587 Z= 0.152 Angle : 0.595 8.172 11783 Z= 0.314 Chirality : 0.043 0.205 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.562 160.913 1496 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.07 % Allowed : 26.60 % Favored : 70.33 % 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: -0.13 (0.28), residues: 958 helix: 1.86 (0.34), residues: 248 sheet: -0.67 (0.29), residues: 360 loop : -0.71 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.013 0.001 TYR B 249 PHE 0.028 0.001 PHE E 552 TRP 0.016 0.001 TRP C 28 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8584) covalent geometry : angle 0.59459 / 0.31 (11777) SS BOND : bond 0.00439 / 0.23 ( 3) SS BOND : angle 1.47674 / 0.72 ( 6) hydrogen bonds : bond 0.04953 / 3.06 ( 331) hydrogen bonds : angle 4.21643 / 3.00 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8569 (mp10) cc_final: 0.8258 (mp10) REVERT: B 199 MET cc_start: 0.8682 (tpt) cc_final: 0.8217 (tpt) REVERT: C 125 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8701 (tm-30) REVERT: D 1 MET cc_start: 0.9051 (ppp) cc_final: 0.8074 (ppp) REVERT: D 119 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7968 (ptp) REVERT: D 168 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8828 (ttpp) REVERT: D 249 TYR cc_start: 0.8977 (m-80) cc_final: 0.8754 (m-10) REVERT: E 377 ARG cc_start: 0.9133 (mpp80) cc_final: 0.8805 (mpp80) REVERT: E 431 MET cc_start: 0.9041 (tpp) cc_final: 0.8689 (tpp) REVERT: E 490 ASN cc_start: 0.9374 (p0) cc_final: 0.9125 (m110) REVERT: E 545 PHE cc_start: 0.9151 (t80) cc_final: 0.8783 (t80) REVERT: E 552 PHE cc_start: 0.9313 (t80) cc_final: 0.9025 (t80) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.0883 time to fit residues: 14.0186 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 0.0670 chunk 32 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.094963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060310 restraints weight = 22659.049| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.53 r_work: 0.2818 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8587 Z= 0.130 Angle : 0.592 10.392 11783 Z= 0.311 Chirality : 0.043 0.211 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.560 160.275 1496 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.19 % Allowed : 26.36 % Favored : 70.45 % 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: -0.09 (0.28), residues: 958 helix: 1.90 (0.34), residues: 248 sheet: -0.63 (0.29), residues: 360 loop : -0.73 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.014 0.001 TYR B 249 PHE 0.027 0.001 PHE E 552 TRP 0.014 0.001 TRP C 28 HIS 0.002 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8584) covalent geometry : angle 0.59127 / 0.31 (11777) SS BOND : bond 0.00551 / 0.28 ( 3) SS BOND : angle 1.56507 / 0.76 ( 6) hydrogen bonds : bond 0.04749 / 2.88 ( 331) hydrogen bonds : angle 4.15409 / 2.95 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.59 seconds wall clock time: 33 minutes 35.29 seconds (2015.29 seconds total)