Starting phenix.real_space_refine on Thu Jul 2 10:32:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg4_45568/07_2026/9cg4_45568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg4_45568/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cg4_45568/07_2026/9cg4_45568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg4_45568/07_2026/9cg4_45568.map" model { file = "/net/cci-nas-00/data/ceres_data/9cg4_45568/07_2026/9cg4_45568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg4_45568/07_2026/9cg4_45568_neut.cif" } 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-dev-6108/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: 2.17, per 1000 atoms: 0.26 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: 0.73 Conformation dependent library (CDL) restraints added in 468.9 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: 0.93 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: 1.35 Time building geometry restraints manager: 0.97 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: 1.130 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- 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 : 0.648 9.606 11783 Z= 0.408 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 0.64710 / 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 : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1129 time to fit residues: 16.2765 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 : 0.260 ------------------------------------------------------------------------------- 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: 30.0000 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.093793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059267 restraints weight = 22488.126| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.57 r_work: 0.2767 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8587 Z= 0.149 Angle : 0.628 11.036 11783 Z= 0.339 Chirality : 0.044 0.233 1377 Planarity : 0.003 0.032 1358 Dihedral : 19.618 168.444 1498 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.25 % Allowed : 26.24 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 958 helix: 1.53 (0.34), residues: 243 sheet: -1.04 (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 0.026 0.002 TYR E 408 PHE 0.010 0.001 PHE B 169 TRP 0.003 0.001 TRP D 28 HIS 0.006 0.002 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 8584) covalent geometry : angle 0.62706 / 0.34 (11777) SS BOND : bond 0.00532 / 0.28 ( 3) SS BOND : angle 1.43176 / 0.71 ( 6) hydrogen bonds : bond 0.07265 / 4.57 ( 331) hydrogen bonds : angle 5.22888 / 3.78 ( 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 126 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8434 (mp10) cc_final: 0.8152 (mp10) REVERT: B 232 ASP cc_start: 0.8839 (t0) cc_final: 0.8547 (p0) REVERT: C 21 ASP cc_start: 0.9155 (m-30) cc_final: 0.8921 (m-30) REVERT: C 41 ASP cc_start: 0.8316 (t0) cc_final: 0.7894 (t0) REVERT: E 377 ARG cc_start: 0.9134 (mpp80) cc_final: 0.8861 (mpp80) REVERT: E 420 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7704 (mmt90) REVERT: E 431 MET cc_start: 0.8851 (tpp) cc_final: 0.8250 (tpp) REVERT: E 490 ASN cc_start: 0.9386 (p0) cc_final: 0.9072 (m110) outliers start: 19 outliers final: 9 residues processed: 121 average time/residue: 0.1054 time to fit residues: 16.9897 Evaluate side-chains 104 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 LEU 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 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: 0.0670 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.059936 restraints weight = 22207.619| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.52 r_work: 0.2777 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8587 Z= 0.133 Angle : 0.583 9.423 11783 Z= 0.314 Chirality : 0.043 0.302 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.534 166.835 1496 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.07 % Allowed : 25.30 % Favored : 71.63 % 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: -0.49 (0.28), residues: 958 helix: 1.55 (0.34), residues: 249 sheet: -0.94 (0.29), residues: 351 loop : -0.86 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.042 0.002 TYR E 408 PHE 0.009 0.001 PHE B 169 TRP 0.004 0.000 TRP C 28 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8584) covalent geometry : angle 0.58285 / 0.31 (11777) SS BOND : bond 0.00597 / 0.31 ( 3) SS BOND : angle 1.14646 / 0.58 ( 6) hydrogen bonds : bond 0.06369 / 3.95 ( 331) hydrogen bonds : angle 4.80319 / 3.45 ( 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: 26 poor density : 106 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8485 (mp10) cc_final: 0.8191 (mp10) REVERT: B 199 MET cc_start: 0.8566 (tpt) cc_final: 0.8332 (tpt) REVERT: B 232 ASP cc_start: 0.8812 (t0) cc_final: 0.8541 (p0) REVERT: C 28 TRP cc_start: 0.8917 (t-100) cc_final: 0.8575 (m100) REVERT: C 40 MET cc_start: 0.8852 (tpp) cc_final: 0.8372 (tpp) REVERT: C 41 ASP cc_start: 0.8307 (t0) cc_final: 0.7814 (t0) REVERT: C 61 ARG cc_start: 0.8362 (ttt-90) cc_final: 0.7868 (ttp80) REVERT: D 1 MET cc_start: 0.8767 (ppp) cc_final: 0.7628 (ppp) REVERT: E 377 ARG cc_start: 0.9137 (mpp80) cc_final: 0.8831 (mpp80) REVERT: E 431 MET cc_start: 0.8952 (tpp) cc_final: 0.8183 (tpp) REVERT: E 490 ASN cc_start: 0.9405 (p0) cc_final: 0.9127 (m110) REVERT: E 545 PHE cc_start: 0.9153 (t80) cc_final: 0.8899 (t80) outliers start: 26 outliers final: 16 residues processed: 127 average time/residue: 0.1060 time to fit residues: 18.1690 Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 CYS 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 450 LEU 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: 8.9990 chunk 44 optimal weight: 0.0030 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.094806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060772 restraints weight = 22581.936| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.44 r_work: 0.2840 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8587 Z= 0.116 Angle : 0.558 8.623 11783 Z= 0.301 Chirality : 0.042 0.214 1377 Planarity : 0.003 0.032 1358 Dihedral : 19.542 164.679 1496 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.78 % Allowed : 25.41 % 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: -0.34 (0.28), residues: 958 helix: 1.70 (0.34), residues: 250 sheet: -0.83 (0.29), residues: 351 loop : -0.83 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.008 0.001 TYR C 249 PHE 0.013 0.001 PHE E 407 TRP 0.007 0.001 TRP E 512 HIS 0.002 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 8584) covalent geometry : angle 0.55773 / 0.30 (11777) SS BOND : bond 0.00502 / 0.26 ( 3) SS BOND : angle 1.11257 / 0.56 ( 6) hydrogen bonds : bond 0.05627 / 3.47 ( 331) hydrogen bonds : angle 4.59944 / 3.30 ( 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 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7630 (ppp) cc_final: 0.7344 (ppp) REVERT: B 198 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: B 199 MET cc_start: 0.8583 (tpt) cc_final: 0.8087 (tpt) REVERT: C 28 TRP cc_start: 0.8976 (t-100) cc_final: 0.8671 (m100) REVERT: C 41 ASP cc_start: 0.8336 (t0) cc_final: 0.7934 (t0) REVERT: C 42 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8741 (p) REVERT: C 61 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.8099 (ttp80) REVERT: D 1 MET cc_start: 0.8943 (ppp) cc_final: 0.7894 (ppp) REVERT: D 68 MET cc_start: 0.8221 (mtm) cc_final: 0.7973 (mpp) REVERT: D 115 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: D 131 GLN cc_start: 0.7962 (pm20) cc_final: 0.7689 (pm20) REVERT: E 377 ARG cc_start: 0.9159 (mpp80) cc_final: 0.8813 (mpp80) REVERT: E 431 MET cc_start: 0.8953 (tpp) cc_final: 0.8191 (tpp) REVERT: E 490 ASN cc_start: 0.9373 (p0) cc_final: 0.9075 (m110) REVERT: E 506 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8341 (mp10) REVERT: E 545 PHE cc_start: 0.9140 (t80) cc_final: 0.8856 (t80) outliers start: 32 outliers final: 16 residues processed: 130 average time/residue: 0.1009 time to fit residues: 17.7485 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 SER 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 115 GLU 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: 0.0570 chunk 81 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.095215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061128 restraints weight = 22384.456| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.47 r_work: 0.2846 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8587 Z= 0.109 Angle : 0.561 8.845 11783 Z= 0.301 Chirality : 0.042 0.214 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.530 164.041 1496 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.02 % Allowed : 24.35 % Favored : 71.63 % 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: -0.28 (0.28), residues: 958 helix: 1.76 (0.34), residues: 250 sheet: -0.76 (0.29), residues: 349 loop : -0.84 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.007 0.001 TYR B 114 PHE 0.010 0.001 PHE E 407 TRP 0.003 0.001 TRP C 28 HIS 0.002 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 8584) covalent geometry : angle 0.56082 / 0.30 (11777) SS BOND : bond 0.00505 / 0.26 ( 3) SS BOND : angle 0.96560 / 0.48 ( 6) hydrogen bonds : bond 0.05283 / 3.23 ( 331) hydrogen bonds : angle 4.40793 / 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 140 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7709 (ppp) cc_final: 0.7498 (ppp) REVERT: B 8 GLN cc_start: 0.8497 (mp10) cc_final: 0.8274 (mp10) REVERT: B 40 MET cc_start: 0.7978 (ptm) cc_final: 0.7766 (ptm) REVERT: B 72 LEU cc_start: 0.9234 (mm) cc_final: 0.8966 (mm) REVERT: B 198 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: B 199 MET cc_start: 0.8578 (tpt) cc_final: 0.8010 (tpt) REVERT: C 28 TRP cc_start: 0.8937 (t-100) cc_final: 0.8685 (m100) REVERT: D 1 MET cc_start: 0.8987 (ppp) cc_final: 0.7937 (ppp) REVERT: D 68 MET cc_start: 0.8295 (mtm) cc_final: 0.8014 (mpp) REVERT: D 115 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8719 (tp30) REVERT: D 131 GLN cc_start: 0.8093 (pm20) cc_final: 0.7833 (pm20) REVERT: D 168 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8809 (ttpp) REVERT: D 249 TYR cc_start: 0.8780 (m-10) cc_final: 0.8463 (m-10) REVERT: E 377 ARG cc_start: 0.9149 (mpp80) cc_final: 0.8810 (mpp80) REVERT: E 420 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7817 (mmt90) REVERT: E 431 MET cc_start: 0.8954 (tpp) cc_final: 0.8033 (mpp) REVERT: E 463 GLN cc_start: 0.8742 (mm110) cc_final: 0.8520 (mm110) REVERT: E 490 ASN cc_start: 0.9340 (p0) cc_final: 0.9015 (m110) REVERT: E 506 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8433 (mp10) REVERT: E 545 PHE cc_start: 0.9127 (t80) cc_final: 0.8824 (t80) outliers start: 34 outliers final: 18 residues processed: 135 average time/residue: 0.1047 time to fit residues: 19.1626 Evaluate side-chains 118 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL 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 115 GLU Chi-restraints excluded: chain D residue 119 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 31 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.095426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061369 restraints weight = 22382.347| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.44 r_work: 0.2853 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8587 Z= 0.109 Angle : 0.559 7.639 11783 Z= 0.300 Chirality : 0.043 0.214 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.527 163.834 1496 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.55 % Allowed : 24.94 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 958 helix: 1.79 (0.34), residues: 250 sheet: -0.71 (0.29), residues: 349 loop : -0.83 (0.30), residues: 359 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 0.007 0.001 PHE E 552 TRP 0.004 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8584) covalent geometry : angle 0.55836 / 0.30 (11777) SS BOND : bond 0.00466 / 0.24 ( 3) SS BOND : angle 0.98002 / 0.49 ( 6) hydrogen bonds : bond 0.05075 / 3.12 ( 331) hydrogen bonds : angle 4.32074 / 3.09 ( 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: 30 poor density : 104 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8490 (mp10) cc_final: 0.8228 (mp10) REVERT: B 72 LEU cc_start: 0.9189 (mm) cc_final: 0.8951 (mm) REVERT: B 198 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: B 199 MET cc_start: 0.8608 (tpt) cc_final: 0.7922 (tpt) REVERT: C 28 TRP cc_start: 0.8929 (t-100) cc_final: 0.8697 (m100) REVERT: C 40 MET cc_start: 0.8917 (tpp) cc_final: 0.8455 (tpp) REVERT: D 1 MET cc_start: 0.8986 (ppp) cc_final: 0.7924 (ppp) REVERT: D 68 MET cc_start: 0.8272 (mtm) cc_final: 0.7974 (mpp) REVERT: D 115 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8706 (tp30) REVERT: D 131 GLN cc_start: 0.8121 (pm20) cc_final: 0.7915 (pm20) REVERT: D 249 TYR cc_start: 0.8821 (m-80) cc_final: 0.8522 (m-10) REVERT: E 377 ARG cc_start: 0.9155 (mpp80) cc_final: 0.8775 (mpp80) REVERT: E 431 MET cc_start: 0.9032 (tpp) cc_final: 0.8465 (tpp) REVERT: E 490 ASN cc_start: 0.9346 (p0) cc_final: 0.9033 (m110) REVERT: E 506 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8421 (mm-40) REVERT: E 545 PHE cc_start: 0.9139 (t80) cc_final: 0.8827 (t80) outliers start: 30 outliers final: 20 residues processed: 128 average time/residue: 0.1020 time to fit residues: 17.7772 Evaluate side-chains 118 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL 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 139 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN 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 115 GLU 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 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 403 ILE 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: 3.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 0.0030 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.094836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.060062 restraints weight = 22918.696| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.52 r_work: 0.2813 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2013 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= 0.155 Angle : 0.581 9.447 11783 Z= 0.309 Chirality : 0.043 0.199 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.558 163.290 1496 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.90 % Allowed : 25.65 % 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: -0.14 (0.28), residues: 958 helix: 1.89 (0.34), residues: 248 sheet: -0.71 (0.29), residues: 349 loop : -0.74 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.011 0.001 TYR B 249 PHE 0.016 0.001 PHE B 2 TRP 0.005 0.001 TRP E 512 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8584) covalent geometry : angle 0.58001 / 0.31 (11777) SS BOND : bond 0.00386 / 0.20 ( 3) SS BOND : angle 1.32228 / 0.65 ( 6) hydrogen bonds : bond 0.05167 / 3.22 ( 331) hydrogen bonds : angle 4.34769 / 3.09 ( 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 : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8538 (mp10) cc_final: 0.8252 (mp10) REVERT: B 198 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: B 199 MET cc_start: 0.8644 (tpt) cc_final: 0.8011 (tpt) REVERT: C 28 TRP cc_start: 0.8961 (t-100) cc_final: 0.8741 (m100) REVERT: C 40 MET cc_start: 0.8981 (tpp) cc_final: 0.8518 (tpp) REVERT: D 1 MET cc_start: 0.8997 (ppp) cc_final: 0.7976 (ppp) REVERT: D 68 MET cc_start: 0.8328 (mtm) cc_final: 0.7988 (mpp) REVERT: D 168 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (ttpp) REVERT: D 249 TYR cc_start: 0.8967 (m-80) cc_final: 0.8669 (m-10) REVERT: E 377 ARG cc_start: 0.9153 (mpp80) cc_final: 0.8811 (mpp80) REVERT: E 490 ASN cc_start: 0.9393 (p0) cc_final: 0.9098 (m110) REVERT: E 506 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8434 (mm-40) REVERT: E 545 PHE cc_start: 0.9154 (t80) cc_final: 0.8838 (t80) outliers start: 33 outliers final: 24 residues processed: 121 average time/residue: 0.0820 time to fit residues: 13.6865 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 GLU 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 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 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 D residue 261 SER 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 472 LEU Chi-restraints excluded: chain E residue 519 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 0.0470 chunk 84 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.095422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.061105 restraints weight = 22640.254| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.46 r_work: 0.2836 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8587 Z= 0.116 Angle : 0.564 8.092 11783 Z= 0.301 Chirality : 0.042 0.211 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.562 163.080 1496 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: -0.11 (0.28), residues: 958 helix: 1.87 (0.34), residues: 248 sheet: -0.68 (0.29), residues: 360 loop : -0.68 (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 0.008 0.001 PHE C 2 TRP 0.004 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 8584) covalent geometry : angle 0.56297 / 0.30 (11777) SS BOND : bond 0.00589 / 0.31 ( 3) SS BOND : angle 1.25100 / 0.61 ( 6) hydrogen bonds : bond 0.04854 / 2.97 ( 331) hydrogen bonds : angle 4.24592 / 3.02 ( 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 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8526 (mp10) cc_final: 0.8231 (mp10) REVERT: B 198 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: B 199 MET cc_start: 0.8641 (tpt) cc_final: 0.8062 (tpt) REVERT: C 28 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.8725 (m100) REVERT: C 40 MET cc_start: 0.8908 (tpp) cc_final: 0.8360 (tpp) REVERT: D 1 MET cc_start: 0.9001 (ppp) cc_final: 0.7985 (ppp) REVERT: D 68 MET cc_start: 0.8382 (mtm) cc_final: 0.8052 (mpp) REVERT: D 119 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7807 (ptp) REVERT: D 168 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8804 (ttpp) REVERT: D 249 TYR cc_start: 0.8909 (m-80) cc_final: 0.8634 (m-10) REVERT: E 377 ARG cc_start: 0.9165 (mpp80) cc_final: 0.8829 (mpp80) REVERT: E 490 ASN cc_start: 0.9380 (p0) cc_final: 0.9073 (m110) REVERT: E 545 PHE cc_start: 0.9142 (t80) cc_final: 0.8820 (t80) outliers start: 34 outliers final: 20 residues processed: 128 average time/residue: 0.0772 time to fit residues: 13.7683 Evaluate side-chains 120 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 28 TRP 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 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 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 235 LEU Chi-restraints excluded: chain D residue 261 SER 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: 0.6980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.095895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061282 restraints weight = 22795.602| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.53 r_work: 0.2842 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8587 Z= 0.114 Angle : 0.575 8.053 11783 Z= 0.304 Chirality : 0.043 0.214 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.551 163.194 1496 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.31 % Allowed : 26.60 % Favored : 70.09 % 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: -0.07 (0.28), residues: 958 helix: 1.89 (0.34), residues: 248 sheet: -0.58 (0.29), residues: 349 loop : -0.74 (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 0.008 0.001 PHE C 2 TRP 0.008 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8584) covalent geometry : angle 0.57390 / 0.30 (11777) SS BOND : bond 0.00509 / 0.26 ( 3) SS BOND : angle 1.31779 / 0.64 ( 6) hydrogen bonds : bond 0.04771 / 2.89 ( 331) hydrogen bonds : angle 4.18705 / 2.98 ( 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 127 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8545 (mp10) cc_final: 0.8233 (mp10) REVERT: B 40 MET cc_start: 0.7806 (ptm) cc_final: 0.7535 (ptm) REVERT: B 198 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: B 199 MET cc_start: 0.8643 (tpt) cc_final: 0.8065 (tpt) REVERT: C 28 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8708 (m100) REVERT: D 1 MET cc_start: 0.8973 (ppp) cc_final: 0.8000 (ppp) REVERT: D 68 MET cc_start: 0.8240 (mtm) cc_final: 0.7932 (mpp) REVERT: D 119 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7816 (ptp) REVERT: D 168 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8803 (ttpp) REVERT: D 249 TYR cc_start: 0.8891 (m-80) cc_final: 0.8628 (m-10) REVERT: E 377 ARG cc_start: 0.9175 (mpp80) cc_final: 0.8832 (mpp80) REVERT: E 490 ASN cc_start: 0.9380 (p0) cc_final: 0.9081 (m110) REVERT: E 545 PHE cc_start: 0.9119 (t80) cc_final: 0.8787 (t80) outliers start: 28 outliers final: 20 residues processed: 121 average time/residue: 0.0793 time to fit residues: 13.2506 Evaluate side-chains 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 B residue 198 GLU Chi-restraints excluded: chain C residue 28 TRP 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 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 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 D residue 261 SER Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 446 VAL 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: 0.9990 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 0.0370 chunk 98 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.095898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061044 restraints weight = 22865.042| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.57 r_work: 0.2837 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2268 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= 0.121 Angle : 0.585 8.710 11783 Z= 0.309 Chirality : 0.043 0.212 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.552 163.176 1496 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.84 % Allowed : 26.83 % 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: -0.07 (0.28), residues: 958 helix: 1.82 (0.34), residues: 248 sheet: -0.58 (0.29), residues: 360 loop : -0.68 (0.32), residues: 350 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 0.008 0.001 PHE C 2 TRP 0.005 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8584) covalent geometry : angle 0.58372 / 0.31 (11777) SS BOND : bond 0.00493 / 0.25 ( 3) SS BOND : angle 1.48063 / 0.71 ( 6) hydrogen bonds : bond 0.04782 / 2.90 ( 331) hydrogen bonds : angle 4.17761 / 2.97 ( 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 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8485 (mp10) cc_final: 0.8172 (mp10) REVERT: B 198 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: B 199 MET cc_start: 0.8664 (tpt) cc_final: 0.8097 (tpt) REVERT: C 28 TRP cc_start: 0.8946 (OUTLIER) cc_final: 0.8738 (m100) REVERT: D 1 MET cc_start: 0.9004 (ppp) cc_final: 0.8036 (ppp) REVERT: D 68 MET cc_start: 0.8302 (mtm) cc_final: 0.7999 (mpp) REVERT: D 119 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7854 (ptp) REVERT: D 249 TYR cc_start: 0.8902 (m-80) cc_final: 0.8650 (m-10) REVERT: E 377 ARG cc_start: 0.9178 (mpp80) cc_final: 0.8819 (mpp80) REVERT: E 490 ASN cc_start: 0.9372 (p0) cc_final: 0.9072 (m110) REVERT: E 545 PHE cc_start: 0.9113 (t80) cc_final: 0.8774 (t80) REVERT: E 552 PHE cc_start: 0.9239 (t80) cc_final: 0.8896 (t80) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 0.0820 time to fit residues: 12.6230 Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 B residue 198 GLU Chi-restraints excluded: chain C residue 28 TRP 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 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 162 CYS 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 261 SER Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.096257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061660 restraints weight = 22577.676| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.52 r_work: 0.2851 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8587 Z= 0.113 Angle : 0.587 10.701 11783 Z= 0.308 Chirality : 0.042 0.217 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.540 163.192 1496 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.36 % Allowed : 27.54 % Favored : 70.09 % 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: -0.05 (0.28), residues: 958 helix: 1.87 (0.34), residues: 248 sheet: -0.56 (0.29), residues: 360 loop : -0.70 (0.32), residues: 350 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 0.007 0.001 PHE C 2 TRP 0.005 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8584) covalent geometry : angle 0.58609 / 0.31 (11777) SS BOND : bond 0.00583 / 0.30 ( 3) SS BOND : angle 1.53414 / 0.73 ( 6) hydrogen bonds : bond 0.04671 / 2.80 ( 331) hydrogen bonds : angle 4.11352 / 2.92 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2342.84 seconds wall clock time: 40 minutes 49.88 seconds (2449.88 seconds total)