Starting phenix.real_space_refine on Sun May 11 19:26:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg4_45568/05_2025/9cg4_45568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg4_45568/05_2025/9cg4_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_45568/05_2025/9cg4_45568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg4_45568/05_2025/9cg4_45568.map" model { file = "/net/cci-nas-00/data/ceres_data/9cg4_45568/05_2025/9cg4_45568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg4_45568/05_2025/9cg4_45568_neut.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.60, per 1000 atoms: 0.67 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.25 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: 2.80 Time building geometry restraints manager: 2.64 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=" CB GLN E 399 " pdb=" CG GLN E 399 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C3' DG F 26 " pdb=" O3' DG F 26 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CA ASP B 232 " pdb=" CB ASP B 232 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.42e+00 bond pdb=" C ALA E 474 " pdb=" N PRO E 475 " ideal model delta sigma weight residual 1.336 1.349 -0.014 1.23e-02 6.61e+03 1.26e+00 bond pdb=" CB GLN C 125 " pdb=" CG GLN C 125 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11557 1.92 - 3.84: 175 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=" CA GLN E 399 " pdb=" CB GLN E 399 " pdb=" CG GLN E 399 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA GLN B 108 " pdb=" CB GLN B 108 " pdb=" CG GLN B 108 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET B 1 " pdb=" CB MET B 1 " pdb=" CG MET B 1 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLN D 108 " pdb=" CB GLN D 108 " pdb=" CG GLN D 108 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 ... (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: 948 0.035 - 0.071: 301 0.071 - 0.106: 93 0.106 - 0.141: 31 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: 0.830 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8587 Z= 0.139 Angle : 0.607 9.606 11783 Z= 0.316 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP C 28 HIS 0.002 0.001 HIS C 44 PHE 0.011 0.001 PHE B 169 TYR 0.016 0.001 TYR B 249 ARG 0.006 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.27926 ( 331) hydrogen bonds : angle 7.92649 ( 876) SS BOND : bond 0.00463 ( 3) SS BOND : angle 1.58153 ( 6) covalent geometry : bond 0.00309 ( 8584) covalent geometry : angle 0.60608 (11777) *********************** 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 : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.2521 time to fit residues: 36.2440 Evaluate side-chains 98 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 84 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 213 ASN D 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058839 restraints weight = 22188.045| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.54 r_work: 0.2760 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1359 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= 0.154 Angle : 0.590 9.823 11783 Z= 0.314 Chirality : 0.042 0.162 1377 Planarity : 0.003 0.032 1358 Dihedral : 19.230 165.230 1498 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.48 % Allowed : 26.36 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 958 helix: 1.57 (0.34), residues: 248 sheet: -1.03 (0.29), residues: 351 loop : -0.79 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 512 HIS 0.002 0.001 HIS C 44 PHE 0.008 0.001 PHE B 169 TYR 0.034 0.002 TYR E 408 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 331) hydrogen bonds : angle 4.90712 ( 876) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.30977 ( 6) covalent geometry : bond 0.00347 ( 8584) covalent geometry : angle 0.58986 (11777) *********************** 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 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8532 (mp10) cc_final: 0.8246 (mp10) REVERT: B 199 MET cc_start: 0.8692 (tpt) cc_final: 0.8449 (tpt) REVERT: B 232 ASP cc_start: 0.8827 (t0) cc_final: 0.8540 (p0) REVERT: C 28 TRP cc_start: 0.8974 (t-100) cc_final: 0.8623 (m100) REVERT: C 41 ASP cc_start: 0.8437 (t0) cc_final: 0.8048 (t0) REVERT: C 61 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.7892 (ttp80) REVERT: E 377 ARG cc_start: 0.9155 (mpp80) cc_final: 0.8849 (mpp80) REVERT: E 420 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7649 (mmt90) REVERT: E 431 MET cc_start: 0.8973 (tpp) cc_final: 0.8490 (tpp) REVERT: E 490 ASN cc_start: 0.9392 (p0) cc_final: 0.9092 (m-40) REVERT: E 545 PHE cc_start: 0.9196 (t80) cc_final: 0.8907 (t80) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 0.2362 time to fit residues: 39.6709 Evaluate side-chains 109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL 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 70 VAL Chi-restraints excluded: chain D residue 98 THR 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 446 VAL Chi-restraints excluded: chain E residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.093210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059129 restraints weight = 22320.083| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.51 r_work: 0.2765 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1737 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= 0.138 Angle : 0.559 8.850 11783 Z= 0.298 Chirality : 0.041 0.205 1377 Planarity : 0.003 0.032 1358 Dihedral : 19.143 157.591 1496 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.43 % Allowed : 25.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 958 helix: 1.82 (0.34), residues: 248 sheet: -0.98 (0.29), residues: 355 loop : -0.76 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 512 HIS 0.002 0.001 HIS C 153 PHE 0.008 0.001 PHE E 552 TYR 0.045 0.002 TYR E 408 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 331) hydrogen bonds : angle 4.52797 ( 876) SS BOND : bond 0.00547 ( 3) SS BOND : angle 1.01234 ( 6) covalent geometry : bond 0.00311 ( 8584) covalent geometry : angle 0.55909 (11777) *********************** 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 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8561 (mp10) cc_final: 0.8232 (mp10) REVERT: B 199 MET cc_start: 0.8731 (tpt) cc_final: 0.8395 (tpt) REVERT: B 232 ASP cc_start: 0.8862 (t0) cc_final: 0.8615 (p0) REVERT: C 28 TRP cc_start: 0.8936 (t-100) cc_final: 0.8628 (m100) REVERT: C 40 MET cc_start: 0.8735 (tpp) cc_final: 0.8300 (tpp) REVERT: C 41 ASP cc_start: 0.8498 (t0) cc_final: 0.7852 (t0) REVERT: C 42 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (p) REVERT: C 44 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8482 (t-90) REVERT: D 1 MET cc_start: 0.8797 (ppp) cc_final: 0.7529 (ppp) REVERT: D 68 MET cc_start: 0.8006 (mtm) cc_final: 0.7773 (mpp) REVERT: D 249 TYR cc_start: 0.8878 (m-80) cc_final: 0.8557 (m-10) REVERT: E 377 ARG cc_start: 0.9176 (mpp80) cc_final: 0.8802 (mpp80) REVERT: E 490 ASN cc_start: 0.9424 (p0) cc_final: 0.9199 (m-40) REVERT: E 506 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8295 (mp10) REVERT: E 545 PHE cc_start: 0.9156 (t80) cc_final: 0.8876 (t80) outliers start: 29 outliers final: 18 residues processed: 128 average time/residue: 0.2351 time to fit residues: 40.0100 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 C residue 42 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 44 HIS 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 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 E residue 382 VAL Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 4 optimal weight: 0.0770 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058409 restraints weight = 22946.059| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.51 r_work: 0.2774 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8587 Z= 0.177 Angle : 0.575 6.734 11783 Z= 0.306 Chirality : 0.041 0.163 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.181 156.219 1496 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.73 % Allowed : 24.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 958 helix: 1.97 (0.33), residues: 247 sheet: -0.91 (0.29), residues: 355 loop : -0.73 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 512 HIS 0.003 0.001 HIS C 44 PHE 0.011 0.001 PHE B 2 TYR 0.013 0.001 TYR B 249 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 331) hydrogen bonds : angle 4.44631 ( 876) SS BOND : bond 0.00431 ( 3) SS BOND : angle 1.26710 ( 6) covalent geometry : bond 0.00406 ( 8584) covalent geometry : angle 0.57447 (11777) *********************** 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 139 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8696 (mp10) cc_final: 0.8354 (mp10) REVERT: B 199 MET cc_start: 0.8671 (tpt) cc_final: 0.8218 (tpt) REVERT: C 28 TRP cc_start: 0.8997 (t-100) cc_final: 0.8734 (m100) REVERT: C 40 MET cc_start: 0.8690 (tpp) cc_final: 0.8351 (tpp) REVERT: D 1 MET cc_start: 0.8988 (ppp) cc_final: 0.7847 (ppp) REVERT: D 68 MET cc_start: 0.8385 (mtm) cc_final: 0.8149 (mpp) REVERT: D 119 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7926 (ptp) REVERT: D 199 MET cc_start: 0.8154 (tpp) cc_final: 0.7941 (mmt) REVERT: D 204 GLN cc_start: 0.9267 (tt0) cc_final: 0.9035 (tt0) REVERT: E 490 ASN cc_start: 0.9400 (p0) cc_final: 0.9185 (m110) REVERT: E 506 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8476 (mp10) REVERT: E 545 PHE cc_start: 0.9186 (t80) cc_final: 0.8871 (t80) outliers start: 40 outliers final: 23 residues processed: 132 average time/residue: 0.2211 time to fit residues: 39.4507 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 : 0.947 ------------------------------------------------------------------------------- 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 C residue 16 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 ASP 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 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 VAL 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 E residue 382 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 519 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 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 = 0.3732 r_free = 0.3732 target = 0.092626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058080 restraints weight = 22714.340| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.51 r_work: 0.2764 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8587 Z= 0.183 Angle : 0.586 7.960 11783 Z= 0.311 Chirality : 0.042 0.178 1377 Planarity : 0.003 0.034 1358 Dihedral : 19.212 154.073 1496 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.49 % Allowed : 24.35 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 958 helix: 2.05 (0.33), residues: 247 sheet: -0.86 (0.29), residues: 351 loop : -0.74 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 28 HIS 0.002 0.001 HIS B 44 PHE 0.015 0.001 PHE E 379 TYR 0.016 0.001 TYR B 249 ARG 0.005 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 331) hydrogen bonds : angle 4.44619 ( 876) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.65088 ( 6) covalent geometry : bond 0.00421 ( 8584) covalent geometry : angle 0.58482 (11777) *********************** 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 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.7962 (ptm) cc_final: 0.6948 (ppp) REVERT: B 199 MET cc_start: 0.8761 (tpt) cc_final: 0.8367 (tpt) REVERT: D 1 MET cc_start: 0.9003 (ppp) cc_final: 0.7989 (ppp) REVERT: D 28 TRP cc_start: 0.9023 (m100) cc_final: 0.8720 (m100) REVERT: D 68 MET cc_start: 0.8333 (mtm) cc_final: 0.8072 (mpp) REVERT: D 119 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7975 (ptp) REVERT: D 204 GLN cc_start: 0.9269 (tt0) cc_final: 0.9029 (tt0) REVERT: E 377 ARG cc_start: 0.9176 (mpp80) cc_final: 0.8860 (mpp80) REVERT: E 545 PHE cc_start: 0.9186 (t80) cc_final: 0.8850 (t80) outliers start: 38 outliers final: 25 residues processed: 128 average time/residue: 0.2249 time to fit residues: 38.7949 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 C residue 12 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 VAL 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 70 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 126 LEU 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 432 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 530 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059099 restraints weight = 22312.339| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.54 r_work: 0.2764 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2352 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= 0.118 Angle : 0.557 7.113 11783 Z= 0.296 Chirality : 0.041 0.175 1377 Planarity : 0.003 0.036 1358 Dihedral : 19.100 153.359 1496 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.66 % Allowed : 26.12 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 958 helix: 2.05 (0.33), residues: 248 sheet: -0.80 (0.29), residues: 360 loop : -0.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 PHE 0.009 0.001 PHE E 379 TYR 0.015 0.001 TYR B 249 ARG 0.005 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 331) hydrogen bonds : angle 4.19645 ( 876) SS BOND : bond 0.00513 ( 3) SS BOND : angle 0.93501 ( 6) covalent geometry : bond 0.00263 ( 8584) covalent geometry : angle 0.55700 (11777) *********************** 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 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7408 (ppp) cc_final: 0.7082 (ppp) REVERT: B 199 MET cc_start: 0.8784 (tpt) cc_final: 0.8357 (tpt) REVERT: C 17 GLU cc_start: 0.9439 (tp30) cc_final: 0.9188 (pt0) REVERT: D 1 MET cc_start: 0.8919 (ppp) cc_final: 0.7871 (ppp) REVERT: D 28 TRP cc_start: 0.8886 (m100) cc_final: 0.8587 (m100) REVERT: D 68 MET cc_start: 0.8167 (mtm) cc_final: 0.7882 (mpp) REVERT: D 119 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7838 (ptp) REVERT: D 204 GLN cc_start: 0.9331 (tt0) cc_final: 0.9090 (tt0) REVERT: E 545 PHE cc_start: 0.9166 (t80) cc_final: 0.8837 (t80) outliers start: 31 outliers final: 17 residues processed: 125 average time/residue: 0.2073 time to fit residues: 35.3508 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 197 ILE 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 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 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 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 65 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 9 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3765 r_free = 0.3765 target = 0.093281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059322 restraints weight = 22334.516| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.44 r_work: 0.2810 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8587 Z= 0.129 Angle : 0.567 6.947 11783 Z= 0.301 Chirality : 0.041 0.168 1377 Planarity : 0.003 0.037 1358 Dihedral : 19.037 151.590 1496 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.43 % Allowed : 26.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 958 helix: 2.10 (0.34), residues: 248 sheet: -0.77 (0.28), residues: 360 loop : -0.59 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 512 HIS 0.002 0.001 HIS C 44 PHE 0.008 0.001 PHE E 379 TYR 0.013 0.001 TYR B 249 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 331) hydrogen bonds : angle 4.16287 ( 876) SS BOND : bond 0.00455 ( 3) SS BOND : angle 1.16839 ( 6) covalent geometry : bond 0.00292 ( 8584) covalent geometry : angle 0.56695 (11777) *********************** 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 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7630 (ppp) cc_final: 0.7342 (ppp) REVERT: B 40 MET cc_start: 0.7970 (ptm) cc_final: 0.7136 (ppp) REVERT: B 199 MET cc_start: 0.8766 (tpt) cc_final: 0.8326 (tpt) REVERT: C 17 GLU cc_start: 0.9438 (tp30) cc_final: 0.9225 (pt0) REVERT: C 28 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (m100) REVERT: D 1 MET cc_start: 0.9002 (ppp) cc_final: 0.7965 (ppp) REVERT: D 28 TRP cc_start: 0.9023 (m100) cc_final: 0.8761 (m100) REVERT: D 68 MET cc_start: 0.8412 (mtm) cc_final: 0.8138 (mpp) REVERT: D 119 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8068 (ptp) REVERT: D 204 GLN cc_start: 0.9284 (tt0) cc_final: 0.9052 (tt0) REVERT: E 545 PHE cc_start: 0.9149 (t80) cc_final: 0.8794 (t80) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.2323 time to fit residues: 38.0026 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 : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 158 VAL 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 123 VAL Chi-restraints excluded: chain D residue 126 LEU 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 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.059381 restraints weight = 22407.103| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.62 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8587 Z= 0.117 Angle : 0.562 6.552 11783 Z= 0.298 Chirality : 0.041 0.160 1377 Planarity : 0.003 0.039 1358 Dihedral : 18.966 150.278 1496 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.78 % Allowed : 25.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 958 helix: 2.14 (0.34), residues: 250 sheet: -0.71 (0.28), residues: 359 loop : -0.65 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 512 HIS 0.002 0.000 HIS C 44 PHE 0.008 0.001 PHE E 379 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 331) hydrogen bonds : angle 4.05856 ( 876) SS BOND : bond 0.00436 ( 3) SS BOND : angle 1.22977 ( 6) covalent geometry : bond 0.00260 ( 8584) covalent geometry : angle 0.56124 (11777) *********************** 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 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7347 (ppp) cc_final: 0.7098 (ppp) REVERT: B 40 MET cc_start: 0.7727 (ptm) cc_final: 0.6722 (ppp) REVERT: B 199 MET cc_start: 0.8624 (tpt) cc_final: 0.8227 (tpt) REVERT: C 28 TRP cc_start: 0.8748 (OUTLIER) cc_final: 0.6942 (m-90) REVERT: D 1 MET cc_start: 0.8940 (ppp) cc_final: 0.7897 (ppp) REVERT: D 28 TRP cc_start: 0.8796 (m100) cc_final: 0.8475 (m100) REVERT: D 68 MET cc_start: 0.8055 (mtm) cc_final: 0.7696 (mpp) REVERT: D 119 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7778 (ptp) REVERT: D 204 GLN cc_start: 0.9137 (tt0) cc_final: 0.8867 (tt0) REVERT: E 545 PHE cc_start: 0.9047 (t80) cc_final: 0.8691 (t80) REVERT: E 547 ARG cc_start: 0.6741 (mtp180) cc_final: 0.6087 (mtp180) outliers start: 32 outliers final: 24 residues processed: 123 average time/residue: 0.2082 time to fit residues: 34.8925 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 : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 197 ILE 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 123 VAL Chi-restraints excluded: chain D residue 126 LEU 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 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 29 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3715 r_free = 0.3715 target = 0.091547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056906 restraints weight = 23209.110| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.54 r_work: 0.2738 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8587 Z= 0.261 Angle : 0.671 12.878 11783 Z= 0.351 Chirality : 0.043 0.158 1377 Planarity : 0.003 0.038 1358 Dihedral : 19.201 149.664 1496 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.90 % Allowed : 25.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 958 helix: 2.10 (0.34), residues: 247 sheet: -0.79 (0.29), residues: 357 loop : -0.63 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 28 HIS 0.005 0.001 HIS C 44 PHE 0.014 0.002 PHE B 2 TYR 0.018 0.002 TYR B 249 ARG 0.006 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 331) hydrogen bonds : angle 4.49918 ( 876) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.84693 ( 6) covalent geometry : bond 0.00603 ( 8584) covalent geometry : angle 0.67030 (11777) *********************** 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 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8039 (ptm) cc_final: 0.7052 (ppp) REVERT: B 199 MET cc_start: 0.8641 (tpt) cc_final: 0.8240 (tpt) REVERT: D 1 MET cc_start: 0.9033 (ppp) cc_final: 0.8049 (ppp) REVERT: D 68 MET cc_start: 0.8420 (mtm) cc_final: 0.8153 (mpp) REVERT: D 204 GLN cc_start: 0.9286 (tt0) cc_final: 0.9044 (tt0) REVERT: E 377 ARG cc_start: 0.9219 (mpp80) cc_final: 0.8873 (mpp80) REVERT: E 545 PHE cc_start: 0.9168 (t80) cc_final: 0.8838 (t80) REVERT: E 552 PHE cc_start: 0.9222 (t80) cc_final: 0.8867 (t80) outliers start: 33 outliers final: 26 residues processed: 113 average time/residue: 0.2169 time to fit residues: 33.4640 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 43 SER 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 123 VAL Chi-restraints excluded: chain D residue 126 LEU 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 Chi-restraints excluded: chain E residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3741 r_free = 0.3741 target = 0.093127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058811 restraints weight = 22280.348| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.59 r_work: 0.2761 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8587 Z= 0.125 Angle : 0.608 10.423 11783 Z= 0.319 Chirality : 0.042 0.164 1377 Planarity : 0.003 0.039 1358 Dihedral : 19.055 148.586 1496 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.84 % Allowed : 26.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 958 helix: 2.20 (0.34), residues: 247 sheet: -0.70 (0.29), residues: 359 loop : -0.67 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.001 0.000 HIS D 246 PHE 0.015 0.001 PHE E 407 TYR 0.010 0.001 TYR C 211 ARG 0.006 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 331) hydrogen bonds : angle 4.13888 ( 876) SS BOND : bond 0.00564 ( 3) SS BOND : angle 1.17646 ( 6) covalent geometry : bond 0.00284 ( 8584) covalent geometry : angle 0.60749 (11777) ********************** 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 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.7810 (ptm) cc_final: 0.6910 (ppp) REVERT: B 199 MET cc_start: 0.8809 (tpt) cc_final: 0.8430 (tpt) REVERT: C 17 GLU cc_start: 0.9395 (tp30) cc_final: 0.9171 (pt0) REVERT: C 28 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.6998 (m-90) REVERT: D 1 MET cc_start: 0.8919 (ppp) cc_final: 0.7872 (ppp) REVERT: D 68 MET cc_start: 0.8213 (mtm) cc_final: 0.7955 (mpp) REVERT: D 119 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7857 (ptp) REVERT: D 199 MET cc_start: 0.7556 (mmt) cc_final: 0.7296 (mmp) REVERT: D 204 GLN cc_start: 0.9387 (tt0) cc_final: 0.9168 (tt0) REVERT: E 545 PHE cc_start: 0.9144 (t80) cc_final: 0.8804 (t80) REVERT: E 547 ARG cc_start: 0.6924 (mtp180) cc_final: 0.6082 (mtp180) REVERT: E 552 PHE cc_start: 0.9126 (t80) cc_final: 0.8780 (t80) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.2190 time to fit residues: 32.4587 Evaluate side-chains 111 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 28 TRP 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 123 VAL Chi-restraints excluded: chain D residue 126 LEU 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 446 VAL Chi-restraints excluded: chain E residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS E 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058949 restraints weight = 22594.433| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.61 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2824 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= 0.130 Angle : 0.599 11.701 11783 Z= 0.314 Chirality : 0.041 0.156 1377 Planarity : 0.003 0.039 1358 Dihedral : 18.957 147.747 1496 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.60 % Allowed : 26.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 958 helix: 2.22 (0.34), residues: 247 sheet: -0.64 (0.29), residues: 359 loop : -0.64 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 28 HIS 0.002 0.000 HIS C 44 PHE 0.013 0.001 PHE E 407 TYR 0.014 0.001 TYR B 249 ARG 0.006 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 331) hydrogen bonds : angle 4.03500 ( 876) SS BOND : bond 0.00476 ( 3) SS BOND : angle 1.35403 ( 6) covalent geometry : bond 0.00297 ( 8584) covalent geometry : angle 0.59830 (11777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.42 seconds wall clock time: 81 minutes 19.77 seconds (4879.77 seconds total)