Starting phenix.real_space_refine on Wed Sep 17 11:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg4_45568/09_2025/9cg4_45568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg4_45568/09_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_45568/09_2025/9cg4_45568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg4_45568/09_2025/9cg4_45568.map" model { file = "/net/cci-nas-00/data/ceres_data/9cg4_45568/09_2025/9cg4_45568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg4_45568/09_2025/9cg4_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-2.0-5805/lib/python3.9/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: 2.21, 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 409.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.06 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: 1.41 Time building geometry restraints manager: 0.98 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: 1.190 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00309 ( 8584) covalent geometry : angle 0.60608 (11777) SS BOND : bond 0.00463 ( 3) SS BOND : angle 1.58153 ( 6) hydrogen bonds : bond 0.27926 ( 331) hydrogen bonds : angle 7.92649 ( 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 : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1204 time to fit residues: 17.3680 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 : 0.319 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059262 restraints weight = 22424.071| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.52 r_work: 0.2768 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8587 Z= 0.144 Angle : 0.586 9.463 11783 Z= 0.312 Chirality : 0.042 0.165 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.197 165.651 1498 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 aren not related in a simple way. whole: -0.54 (0.28), residues: 958 helix: 1.54 (0.34), residues: 250 sheet: -1.06 (0.29), residues: 353 loop : -0.82 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.034 0.002 TYR E 408 PHE 0.009 0.001 PHE E 407 TRP 0.003 0.001 TRP E 512 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8584) covalent geometry : angle 0.58564 (11777) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.25024 ( 6) hydrogen bonds : bond 0.05834 ( 331) hydrogen bonds : angle 4.87417 ( 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 129 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8522 (mp10) cc_final: 0.8227 (mp10) REVERT: B 199 MET cc_start: 0.8680 (tpt) cc_final: 0.8436 (tpt) REVERT: B 232 ASP cc_start: 0.8827 (t0) cc_final: 0.8554 (p0) REVERT: C 28 TRP cc_start: 0.8971 (t-100) cc_final: 0.8629 (m100) REVERT: C 40 MET cc_start: 0.9171 (tpp) cc_final: 0.8872 (tpp) REVERT: C 41 ASP cc_start: 0.8409 (t0) cc_final: 0.8050 (t0) REVERT: C 61 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.7879 (ttp80) REVERT: E 377 ARG cc_start: 0.9155 (mpp80) cc_final: 0.8835 (mpp80) REVERT: E 420 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7596 (mmt90) REVERT: E 431 MET cc_start: 0.8992 (tpp) cc_final: 0.8529 (tpp) REVERT: E 490 ASN cc_start: 0.9390 (p0) cc_final: 0.9085 (m-40) REVERT: E 545 PHE cc_start: 0.9190 (t80) cc_final: 0.8893 (t80) outliers start: 19 outliers final: 10 residues processed: 126 average time/residue: 0.1111 time to fit residues: 18.5334 Evaluate side-chains 107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.092567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058194 restraints weight = 22225.088| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.50 r_work: 0.2742 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8587 Z= 0.164 Angle : 0.572 8.660 11783 Z= 0.304 Chirality : 0.041 0.172 1377 Planarity : 0.003 0.031 1358 Dihedral : 19.177 156.619 1496 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.19 % Allowed : 26.48 % 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 aren not related in a simple way. whole: -0.32 (0.28), residues: 958 helix: 1.84 (0.34), residues: 248 sheet: -0.94 (0.29), residues: 351 loop : -0.76 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.049 0.002 TYR E 408 PHE 0.008 0.001 PHE B 169 TRP 0.010 0.001 TRP E 512 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8584) covalent geometry : angle 0.57182 (11777) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.07441 ( 6) hydrogen bonds : bond 0.05303 ( 331) hydrogen bonds : angle 4.54856 ( 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 129 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8582 (mp10) cc_final: 0.8247 (mp10) REVERT: B 199 MET cc_start: 0.8712 (tpt) cc_final: 0.8367 (tpt) REVERT: B 232 ASP cc_start: 0.8865 (t0) cc_final: 0.8621 (p0) REVERT: C 17 GLU cc_start: 0.9431 (tp30) cc_final: 0.9211 (pt0) REVERT: C 28 TRP cc_start: 0.8957 (t-100) cc_final: 0.8654 (m100) REVERT: C 42 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8772 (p) REVERT: C 44 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (t70) REVERT: C 61 ARG cc_start: 0.8361 (ttt-90) cc_final: 0.7852 (ttp80) REVERT: D 1 MET cc_start: 0.8825 (ppp) cc_final: 0.7554 (ppp) REVERT: D 68 MET cc_start: 0.8218 (mpp) cc_final: 0.7925 (mpp) REVERT: D 249 TYR cc_start: 0.8925 (m-80) cc_final: 0.8631 (m-10) REVERT: E 377 ARG cc_start: 0.9178 (mpp80) cc_final: 0.8809 (mpp80) REVERT: E 490 ASN cc_start: 0.9426 (p0) cc_final: 0.9218 (m-40) REVERT: E 506 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8313 (mp10) REVERT: E 545 PHE cc_start: 0.9193 (t80) cc_final: 0.8883 (t80) REVERT: E 552 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) outliers start: 27 outliers final: 15 residues processed: 123 average time/residue: 0.1177 time to fit residues: 19.0067 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 197 ILE Chi-restraints excluded: chain C residue 42 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 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 12 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.092411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.057810 restraints weight = 23142.095| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.52 r_work: 0.2758 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8587 Z= 0.194 Angle : 0.587 6.396 11783 Z= 0.310 Chirality : 0.042 0.167 1377 Planarity : 0.003 0.030 1358 Dihedral : 19.234 156.184 1496 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.85 % Allowed : 24.59 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.28), residues: 958 helix: 1.95 (0.33), residues: 247 sheet: -0.97 (0.29), residues: 353 loop : -0.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.010 0.001 TYR C 249 PHE 0.011 0.001 PHE B 2 TRP 0.007 0.001 TRP E 512 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8584) covalent geometry : angle 0.58589 (11777) SS BOND : bond 0.00477 ( 3) SS BOND : angle 1.42104 ( 6) hydrogen bonds : bond 0.05060 ( 331) hydrogen bonds : angle 4.43630 ( 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 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8732 (mp10) cc_final: 0.8391 (mp10) REVERT: B 199 MET cc_start: 0.8741 (tpt) cc_final: 0.8301 (tpt) REVERT: C 17 GLU cc_start: 0.9477 (tp30) cc_final: 0.9224 (pt0) REVERT: C 28 TRP cc_start: 0.9003 (t-100) cc_final: 0.8730 (m100) REVERT: C 41 ASP cc_start: 0.8670 (t0) cc_final: 0.8034 (t0) REVERT: C 44 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8475 (t-90) REVERT: C 61 ARG cc_start: 0.8502 (ttt-90) cc_final: 0.7994 (ttp80) REVERT: D 1 MET cc_start: 0.8986 (ppp) cc_final: 0.7872 (ppp) REVERT: D 98 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9132 (t) REVERT: D 115 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: D 204 GLN cc_start: 0.9254 (tt0) cc_final: 0.9024 (tt0) REVERT: E 490 ASN cc_start: 0.9401 (p0) cc_final: 0.9199 (m110) REVERT: E 506 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8471 (mm-40) REVERT: E 545 PHE cc_start: 0.9177 (t80) cc_final: 0.8867 (t80) REVERT: E 552 PHE cc_start: 0.9101 (t80) cc_final: 0.8828 (t80) outliers start: 41 outliers final: 23 residues processed: 131 average time/residue: 0.0983 time to fit residues: 17.4929 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 79 LEU 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 43 SER Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 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 115 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 MET 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 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: 3.9990 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.093241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058721 restraints weight = 22344.854| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.61 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2249 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= 0.117 Angle : 0.538 6.380 11783 Z= 0.286 Chirality : 0.041 0.157 1377 Planarity : 0.003 0.033 1358 Dihedral : 19.115 154.604 1496 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.55 % Allowed : 25.06 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.28), residues: 958 helix: 2.04 (0.33), residues: 248 sheet: -0.84 (0.28), residues: 360 loop : -0.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.009 0.001 TYR D 249 PHE 0.012 0.001 PHE E 379 TRP 0.006 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8584) covalent geometry : angle 0.53803 (11777) SS BOND : bond 0.00400 ( 3) SS BOND : angle 1.07666 ( 6) hydrogen bonds : bond 0.04402 ( 331) hydrogen bonds : angle 4.15890 ( 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 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7290 (ppp) cc_final: 0.6978 (ppp) REVERT: B 40 MET cc_start: 0.7716 (ptm) cc_final: 0.6711 (ppp) REVERT: B 199 MET cc_start: 0.8629 (tpt) cc_final: 0.8233 (tpt) REVERT: C 28 TRP cc_start: 0.8797 (t-100) cc_final: 0.8428 (m100) REVERT: C 41 ASP cc_start: 0.8267 (t0) cc_final: 0.7634 (t0) REVERT: C 61 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7615 (ttp80) REVERT: D 1 MET cc_start: 0.8923 (ppp) cc_final: 0.7855 (ppp) REVERT: D 68 MET cc_start: 0.8055 (mpp) cc_final: 0.7852 (mpp) REVERT: D 98 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9099 (t) REVERT: D 115 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: D 119 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7629 (ptp) REVERT: D 204 GLN cc_start: 0.9134 (tt0) cc_final: 0.8844 (tt0) REVERT: E 490 ASN cc_start: 0.9421 (p0) cc_final: 0.9201 (m110) REVERT: E 506 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8369 (mm-40) REVERT: E 545 PHE cc_start: 0.9088 (t80) cc_final: 0.8710 (t80) REVERT: E 552 PHE cc_start: 0.9064 (t80) cc_final: 0.8736 (t80) outliers start: 30 outliers final: 17 residues processed: 128 average time/residue: 0.1086 time to fit residues: 18.6533 Evaluate side-chains 118 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 72 LEU 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 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 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 432 THR 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: 9.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.092826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058668 restraints weight = 22499.291| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.47 r_work: 0.2795 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2371 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= 0.140 Angle : 0.557 8.130 11783 Z= 0.296 Chirality : 0.041 0.156 1377 Planarity : 0.003 0.034 1358 Dihedral : 19.081 153.186 1496 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.14 % Allowed : 25.06 % 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 aren not related in a simple way. whole: -0.11 (0.28), residues: 958 helix: 2.02 (0.33), residues: 248 sheet: -0.81 (0.28), residues: 360 loop : -0.63 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.014 0.001 TYR B 249 PHE 0.009 0.001 PHE E 407 TRP 0.004 0.001 TRP E 512 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8584) covalent geometry : angle 0.55685 (11777) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.19742 ( 6) hydrogen bonds : bond 0.04514 ( 331) hydrogen bonds : angle 4.17413 ( 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 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7612 (ppp) cc_final: 0.7366 (ppp) REVERT: B 199 MET cc_start: 0.8743 (tpt) cc_final: 0.8288 (tpt) REVERT: C 41 ASP cc_start: 0.8563 (t0) cc_final: 0.8106 (t0) REVERT: C 61 ARG cc_start: 0.8599 (ttt-90) cc_final: 0.8088 (ttp80) REVERT: C 199 MET cc_start: 0.8797 (tpt) cc_final: 0.8559 (tpt) REVERT: D 1 MET cc_start: 0.8999 (ppp) cc_final: 0.7967 (ppp) REVERT: D 28 TRP cc_start: 0.8950 (m100) cc_final: 0.8640 (m100) REVERT: D 68 MET cc_start: 0.8441 (mpp) cc_final: 0.8134 (mpp) REVERT: D 119 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7964 (ptp) REVERT: D 204 GLN cc_start: 0.9299 (tt0) cc_final: 0.9057 (tt0) REVERT: E 490 ASN cc_start: 0.9393 (p0) cc_final: 0.9178 (m110) REVERT: E 545 PHE cc_start: 0.9148 (t80) cc_final: 0.8811 (t80) outliers start: 35 outliers final: 23 residues processed: 129 average time/residue: 0.1009 time to fit residues: 17.6317 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 72 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 64 ARG 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 432 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 530 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.093626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059031 restraints weight = 22410.381| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.61 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8587 Z= 0.119 Angle : 0.559 8.435 11783 Z= 0.298 Chirality : 0.041 0.155 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.001 151.964 1496 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.28), residues: 958 helix: 2.03 (0.33), residues: 248 sheet: -0.72 (0.28), residues: 359 loop : -0.65 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.013 0.001 TYR B 249 PHE 0.008 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 covalent geometry : bond 0.00265 ( 8584) covalent geometry : angle 0.55852 (11777) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.03281 ( 6) hydrogen bonds : bond 0.04247 ( 331) hydrogen bonds : angle 4.10706 ( 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 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.7737 (ptm) cc_final: 0.6747 (ppp) REVERT: B 199 MET cc_start: 0.8617 (tpt) cc_final: 0.8222 (tpt) REVERT: C 28 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.8555 (m100) REVERT: C 40 MET cc_start: 0.8285 (tpp) cc_final: 0.7810 (tpp) REVERT: C 61 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7665 (ttp80) REVERT: D 1 MET cc_start: 0.8939 (ppp) cc_final: 0.7897 (ppp) REVERT: D 68 MET cc_start: 0.8093 (mpp) cc_final: 0.7829 (mpp) REVERT: D 119 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7704 (ptp) REVERT: D 204 GLN cc_start: 0.9115 (tt0) cc_final: 0.8873 (tt0) REVERT: E 490 ASN cc_start: 0.9426 (p0) cc_final: 0.9206 (m110) REVERT: E 545 PHE cc_start: 0.9016 (t80) cc_final: 0.8695 (t80) REVERT: E 552 PHE cc_start: 0.8999 (t80) cc_final: 0.8669 (t80) outliers start: 32 outliers final: 24 residues processed: 126 average time/residue: 0.1100 time to fit residues: 18.6199 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG 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 43 SER 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 64 ARG 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 432 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 530 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056490 restraints weight = 23095.679| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.48 r_work: 0.2728 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8587 Z= 0.274 Angle : 0.676 8.516 11783 Z= 0.355 Chirality : 0.044 0.157 1377 Planarity : 0.003 0.034 1358 Dihedral : 19.242 150.614 1496 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.37 % Allowed : 25.53 % 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 aren not related in a simple way. whole: -0.19 (0.28), residues: 958 helix: 2.01 (0.33), residues: 247 sheet: -0.96 (0.28), residues: 373 loop : -0.56 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.017 0.002 TYR B 249 PHE 0.013 0.002 PHE B 2 TRP 0.005 0.001 TRP B 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8584) covalent geometry : angle 0.67536 (11777) SS BOND : bond 0.00388 ( 3) SS BOND : angle 1.71619 ( 6) hydrogen bonds : bond 0.05459 ( 331) hydrogen bonds : angle 4.54161 ( 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 122 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8060 (ptm) cc_final: 0.7065 (ppp) REVERT: B 199 MET cc_start: 0.8661 (tpt) cc_final: 0.8262 (tpt) REVERT: C 40 MET cc_start: 0.8637 (tpp) cc_final: 0.8186 (tpp) REVERT: D 1 MET cc_start: 0.9049 (ppp) cc_final: 0.8074 (ppp) REVERT: D 204 GLN cc_start: 0.9280 (tt0) cc_final: 0.9050 (tt0) REVERT: E 377 ARG cc_start: 0.9222 (mpp80) cc_final: 0.8880 (mpp80) REVERT: E 545 PHE cc_start: 0.9160 (t80) cc_final: 0.8843 (t80) REVERT: E 552 PHE cc_start: 0.9145 (t80) cc_final: 0.8858 (t80) outliers start: 37 outliers final: 31 residues processed: 114 average time/residue: 0.1039 time to fit residues: 16.1480 Evaluate side-chains 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 158 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 43 SER 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 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 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 409 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058788 restraints weight = 22378.020| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.65 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8587 Z= 0.118 Angle : 0.587 8.633 11783 Z= 0.311 Chirality : 0.041 0.151 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.025 149.380 1496 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.84 % Allowed : 27.07 % 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 aren not related in a simple way. whole: -0.06 (0.28), residues: 958 helix: 2.06 (0.34), residues: 248 sheet: -0.71 (0.29), residues: 359 loop : -0.70 (0.32), residues: 351 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 0.012 0.001 PHE E 407 TRP 0.006 0.001 TRP D 28 HIS 0.001 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8584) covalent geometry : angle 0.58667 (11777) SS BOND : bond 0.00658 ( 3) SS BOND : angle 1.05325 ( 6) hydrogen bonds : bond 0.04191 ( 331) hydrogen bonds : angle 4.12969 ( 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 118 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.7848 (ptm) cc_final: 0.6810 (ppp) REVERT: B 199 MET cc_start: 0.8657 (tpt) cc_final: 0.8128 (tpt) REVERT: D 1 MET cc_start: 0.8925 (ppp) cc_final: 0.7888 (ppp) REVERT: D 119 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7702 (ptp) REVERT: E 506 GLN cc_start: 0.8522 (mm110) cc_final: 0.8249 (mm-40) REVERT: E 545 PHE cc_start: 0.9009 (t80) cc_final: 0.8710 (t80) REVERT: E 547 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6129 (mtp180) REVERT: E 552 PHE cc_start: 0.9038 (t80) cc_final: 0.8711 (t80) outliers start: 24 outliers final: 17 residues processed: 111 average time/residue: 0.1210 time to fit residues: 18.1522 Evaluate side-chains 111 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 43 SER 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 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 195 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 432 THR 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: 0.8980 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.093459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059242 restraints weight = 22532.931| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.49 r_work: 0.2810 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8587 Z= 0.137 Angle : 0.601 10.258 11783 Z= 0.316 Chirality : 0.041 0.153 1377 Planarity : 0.003 0.035 1358 Dihedral : 18.991 148.734 1496 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.84 % Allowed : 27.07 % 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 aren not related in a simple way. whole: -0.00 (0.28), residues: 958 helix: 2.13 (0.34), residues: 247 sheet: -0.67 (0.29), residues: 359 loop : -0.67 (0.32), residues: 352 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 E 379 TRP 0.004 0.001 TRP D 28 HIS 0.001 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8584) covalent geometry : angle 0.60061 (11777) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.33213 ( 6) hydrogen bonds : bond 0.04345 ( 331) hydrogen bonds : angle 4.09795 ( 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 : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.7988 (ptm) cc_final: 0.7040 (ppp) REVERT: B 199 MET cc_start: 0.8771 (tpt) cc_final: 0.8375 (tpt) REVERT: C 28 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.8762 (m100) REVERT: D 1 MET cc_start: 0.9009 (ppp) cc_final: 0.7989 (ppp) REVERT: D 119 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7970 (ptp) REVERT: D 199 MET cc_start: 0.7570 (mmt) cc_final: 0.7139 (mmp) REVERT: E 506 GLN cc_start: 0.8706 (mm110) cc_final: 0.8447 (mm-40) REVERT: E 545 PHE cc_start: 0.9087 (t80) cc_final: 0.8777 (t80) REVERT: E 552 PHE cc_start: 0.9113 (t80) cc_final: 0.8804 (t80) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.1090 time to fit residues: 16.6805 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU 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 43 SER Chi-restraints excluded: chain C residue 44 HIS 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 126 LEU Chi-restraints excluded: chain D residue 136 VAL 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 409 GLN 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 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 463 GLN E 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.094873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060417 restraints weight = 22208.646| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.63 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2933 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= 0.116 Angle : 0.589 9.460 11783 Z= 0.310 Chirality : 0.041 0.156 1377 Planarity : 0.003 0.036 1358 Dihedral : 18.854 147.530 1496 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.48 % Allowed : 27.66 % 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 aren not related in a simple way. whole: 0.02 (0.28), residues: 958 helix: 2.10 (0.34), residues: 252 sheet: -0.62 (0.29), residues: 359 loop : -0.71 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.008 0.001 TYR B 249 PHE 0.018 0.001 PHE E 407 TRP 0.008 0.001 TRP E 512 HIS 0.001 0.000 HIS D 153 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8584) covalent geometry : angle 0.58822 (11777) SS BOND : bond 0.00458 ( 3) SS BOND : angle 0.99285 ( 6) hydrogen bonds : bond 0.04058 ( 331) hydrogen bonds : angle 3.93741 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.63 seconds wall clock time: 38 minutes 46.91 seconds (2326.91 seconds total)