Starting phenix.real_space_refine on Wed Mar 12 22:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg4_45568/03_2025/9cg4_45568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg4_45568/03_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_45568/03_2025/9cg4_45568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg4_45568/03_2025/9cg4_45568.map" model { file = "/net/cci-nas-00/data/ceres_data/9cg4_45568/03_2025/9cg4_45568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg4_45568/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.93, per 1000 atoms: 0.83 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: 2.47 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: 4.13 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: 2.88 Time building geometry restraints manager: 2.87 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: 1.680 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.960 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- 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 8584 Z= 0.195 Angle : 0.606 9.606 11777 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 *********************** 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 : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.2776 time to fit residues: 40.2471 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 : 0.910 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058836 restraints weight = 22188.048| |-----------------------------------------------------------------------------| 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: 0.8229 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 8584 Z= 0.220 Angle : 0.590 9.823 11777 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 *********************** 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 : 0.873 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: 0.8447 (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: 0.8624 (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: 0.9154 (mpp80) cc_final: 0.8849 (mpp80) REVERT: E 420 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7650 (mmt90) REVERT: E 431 MET cc_start: 0.8972 (tpp) cc_final: 0.8489 (tpp) REVERT: E 490 ASN cc_start: 0.9391 (p0) cc_final: 0.9091 (m-40) REVERT: E 545 PHE cc_start: 0.9195 (t80) cc_final: 0.8906 (t80) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 0.2548 time to fit residues: 42.6348 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 : 0.944 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 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: 0.0050 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057724 restraints weight = 22336.049| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.56 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8584 Z= 0.225 Angle : 0.568 9.229 11777 Z= 0.302 Chirality : 0.041 0.171 1377 Planarity : 0.003 0.032 1358 Dihedral : 19.167 156.199 1496 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.66 % Allowed : 25.65 % 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: -0.36 (0.28), residues: 958 helix: 1.81 (0.34), residues: 248 sheet: -0.98 (0.29), residues: 355 loop : -0.76 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 512 HIS 0.003 0.001 HIS B 153 PHE 0.008 0.001 PHE E 552 TYR 0.049 0.002 TYR E 408 ARG 0.005 0.000 ARG B 146 *********************** 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: 31 poor density : 104 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8485 (mp10) cc_final: 0.8131 (mp10) REVERT: B 199 MET cc_start: 0.8610 (tpt) cc_final: 0.8297 (tpt) REVERT: C 28 TRP cc_start: 0.8847 (t-100) cc_final: 0.8537 (m100) REVERT: C 41 ASP cc_start: 0.8312 (t0) cc_final: 0.7706 (t0) REVERT: C 42 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 44 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8542 (t70) REVERT: D 1 MET cc_start: 0.8854 (ppp) cc_final: 0.7575 (ppp) REVERT: D 249 TYR cc_start: 0.8689 (m-80) cc_final: 0.8388 (m-10) REVERT: E 377 ARG cc_start: 0.9162 (mpp80) cc_final: 0.8788 (mpp80) REVERT: E 488 ASN cc_start: 0.8696 (t0) cc_final: 0.8384 (t0) REVERT: E 506 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8274 (mp10) REVERT: E 545 PHE cc_start: 0.9051 (t80) cc_final: 0.8746 (t80) REVERT: E 552 PHE cc_start: 0.9016 (t80) cc_final: 0.8788 (t80) outliers start: 31 outliers final: 19 residues processed: 128 average time/residue: 0.2754 time to fit residues: 47.1826 Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 21 ASP 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: 0.2980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.093796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059192 restraints weight = 22882.387| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.50 r_work: 0.2791 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8584 Z= 0.205 Angle : 0.553 6.675 11777 Z= 0.295 Chirality : 0.041 0.162 1377 Planarity : 0.003 0.034 1358 Dihedral : 19.144 156.613 1496 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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 (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: 1.93 (0.33), residues: 248 sheet: -0.88 (0.29), residues: 353 loop : -0.75 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 512 HIS 0.002 0.001 HIS C 153 PHE 0.008 0.001 PHE B 169 TYR 0.013 0.001 TYR B 249 ARG 0.004 0.000 ARG B 146 *********************** 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 136 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7650 (ppp) cc_final: 0.7332 (ppp) REVERT: B 199 MET cc_start: 0.8712 (tpt) cc_final: 0.8271 (tpt) REVERT: C 28 TRP cc_start: 0.8991 (t-100) cc_final: 0.8640 (m100) REVERT: D 1 MET cc_start: 0.8977 (ppp) cc_final: 0.7819 (ppp) REVERT: D 68 MET cc_start: 0.8431 (mtm) cc_final: 0.8171 (mpp) REVERT: D 119 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7891 (ptp) REVERT: D 204 GLN cc_start: 0.9288 (tt0) cc_final: 0.9087 (tt0) REVERT: E 488 ASN cc_start: 0.8732 (t0) cc_final: 0.8454 (t0) REVERT: E 545 PHE cc_start: 0.9175 (t80) cc_final: 0.8868 (t80) REVERT: E 552 PHE cc_start: 0.9111 (t80) cc_final: 0.8844 (t80) outliers start: 35 outliers final: 19 residues processed: 130 average time/residue: 0.2126 time to fit residues: 37.6088 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 : 0.958 ------------------------------------------------------------------------------- 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 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 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 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 2 optimal weight: 0.2980 chunk 99 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.094489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060009 restraints weight = 22601.883| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.52 r_work: 0.2810 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8584 Z= 0.171 Angle : 0.548 8.541 11777 Z= 0.293 Chirality : 0.041 0.182 1377 Planarity : 0.003 0.035 1358 Dihedral : 19.085 155.099 1496 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.78 % Allowed : 25.06 % 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: -0.14 (0.28), residues: 958 helix: 2.01 (0.33), residues: 248 sheet: -0.82 (0.28), residues: 360 loop : -0.67 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.002 0.000 HIS B 44 PHE 0.011 0.001 PHE E 379 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG B 146 *********************** 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 132 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7625 (ppp) cc_final: 0.7385 (ppp) REVERT: B 8 GLN cc_start: 0.8584 (mp10) cc_final: 0.8300 (mp10) REVERT: B 40 MET cc_start: 0.8033 (ptm) cc_final: 0.7335 (ppp) REVERT: B 199 MET cc_start: 0.8713 (tpt) cc_final: 0.8263 (tpt) REVERT: C 28 TRP cc_start: 0.8981 (t-100) cc_final: 0.8731 (m100) REVERT: D 1 MET cc_start: 0.9009 (ppp) cc_final: 0.7951 (ppp) REVERT: D 68 MET cc_start: 0.8351 (mtm) cc_final: 0.8099 (mpp) REVERT: D 119 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7934 (ptp) REVERT: D 204 GLN cc_start: 0.9273 (tt0) cc_final: 0.9024 (tt0) REVERT: E 488 ASN cc_start: 0.8747 (t0) cc_final: 0.8440 (t0) REVERT: E 545 PHE cc_start: 0.9174 (t80) cc_final: 0.8841 (t80) REVERT: E 552 PHE cc_start: 0.9127 (t80) cc_final: 0.8826 (t80) outliers start: 32 outliers final: 20 residues processed: 127 average time/residue: 0.2224 time to fit residues: 38.2988 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.093401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059448 restraints weight = 22286.378| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.43 r_work: 0.2808 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.193 Angle : 0.553 8.133 11777 Z= 0.293 Chirality : 0.041 0.176 1377 Planarity : 0.003 0.036 1358 Dihedral : 19.068 153.839 1496 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.78 % Allowed : 25.65 % 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 (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: 2.03 (0.34), residues: 248 sheet: -0.77 (0.28), residues: 360 loop : -0.68 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 512 HIS 0.002 0.000 HIS C 153 PHE 0.007 0.001 PHE E 379 TYR 0.014 0.001 TYR B 249 ARG 0.005 0.000 ARG B 146 *********************** 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 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8649 (mp10) cc_final: 0.8326 (mp10) REVERT: B 199 MET cc_start: 0.8744 (tpt) cc_final: 0.8299 (tpt) REVERT: C 28 TRP cc_start: 0.8975 (t-100) cc_final: 0.8752 (m100) REVERT: D 1 MET cc_start: 0.9011 (ppp) cc_final: 0.7979 (ppp) REVERT: D 68 MET cc_start: 0.8328 (mtm) cc_final: 0.8125 (mpp) REVERT: D 119 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7949 (ptp) REVERT: D 204 GLN cc_start: 0.9273 (tt0) cc_final: 0.9026 (tt0) REVERT: E 488 ASN cc_start: 0.8763 (t0) cc_final: 0.8426 (t0) REVERT: E 545 PHE cc_start: 0.9153 (t80) cc_final: 0.8795 (t80) outliers start: 32 outliers final: 22 residues processed: 119 average time/residue: 0.2146 time to fit residues: 35.1379 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 16 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 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 403 ILE 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 65 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.092732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058152 restraints weight = 22919.232| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.54 r_work: 0.2839 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8584 Z= 0.263 Angle : 0.592 10.029 11777 Z= 0.314 Chirality : 0.042 0.186 1377 Planarity : 0.003 0.036 1358 Dihedral : 19.145 152.216 1496 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.37 % Allowed : 24.82 % 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 (0.33), residues: 247 sheet: -0.79 (0.28), residues: 361 loop : -0.62 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 28 HIS 0.003 0.001 HIS C 44 PHE 0.010 0.001 PHE B 169 TYR 0.016 0.001 TYR B 249 ARG 0.004 0.000 ARG B 146 *********************** 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 132 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8756 (mp10) cc_final: 0.8408 (mp10) REVERT: B 40 MET cc_start: 0.7970 (ptm) cc_final: 0.7104 (ppp) REVERT: B 199 MET cc_start: 0.8654 (tpt) cc_final: 0.8295 (tpt) REVERT: D 1 MET cc_start: 0.9016 (ppp) cc_final: 0.7999 (ppp) REVERT: D 68 MET cc_start: 0.8438 (mtm) cc_final: 0.8210 (mpp) REVERT: D 119 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (ptp) REVERT: D 204 GLN cc_start: 0.9217 (tt0) cc_final: 0.8986 (tt0) REVERT: E 488 ASN cc_start: 0.8774 (t0) cc_final: 0.8412 (t0) REVERT: E 506 GLN cc_start: 0.8765 (mm110) cc_final: 0.8502 (mm-40) REVERT: E 545 PHE cc_start: 0.9160 (t80) cc_final: 0.8796 (t80) REVERT: E 552 PHE cc_start: 0.9105 (t80) cc_final: 0.8806 (t80) outliers start: 37 outliers final: 30 residues processed: 124 average time/residue: 0.2442 time to fit residues: 41.4228 Evaluate side-chains 122 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 88 ILE Chi-restraints excluded: chain B residue 158 VAL 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 139 MET 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 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 THR 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 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 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 76 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.093798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059259 restraints weight = 22390.817| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.66 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8584 Z= 0.157 Angle : 0.557 7.832 11777 Z= 0.296 Chirality : 0.041 0.178 1377 Planarity : 0.003 0.038 1358 Dihedral : 19.005 151.175 1496 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.43 % Allowed : 25.18 % 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 (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: 0.02 (0.28), residues: 958 helix: 2.11 (0.33), residues: 249 sheet: -0.65 (0.29), residues: 359 loop : -0.65 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 PHE 0.007 0.001 PHE E 552 TYR 0.016 0.001 TYR B 249 ARG 0.004 0.000 ARG B 146 *********************** 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 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8545 (mp10) cc_final: 0.8144 (mp10) REVERT: B 40 MET cc_start: 0.7693 (ptm) cc_final: 0.6648 (ppp) REVERT: B 199 MET cc_start: 0.8623 (tpt) cc_final: 0.8230 (tpt) REVERT: C 28 TRP cc_start: 0.8780 (OUTLIER) cc_final: 0.6918 (m-90) REVERT: D 1 MET cc_start: 0.8898 (ppp) cc_final: 0.7844 (ppp) REVERT: D 68 MET cc_start: 0.8010 (mtm) cc_final: 0.7738 (mpp) REVERT: D 119 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7737 (ptp) REVERT: D 204 GLN cc_start: 0.9117 (tt0) cc_final: 0.8881 (tt0) REVERT: E 488 ASN cc_start: 0.8677 (t0) cc_final: 0.8300 (t0) REVERT: E 545 PHE cc_start: 0.9041 (t80) cc_final: 0.8683 (t80) REVERT: E 547 ARG cc_start: 0.6806 (mtp180) cc_final: 0.6169 (mtp180) REVERT: E 552 PHE cc_start: 0.9009 (t80) cc_final: 0.8682 (t80) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.3413 time to fit residues: 59.2991 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL 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 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 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 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.092398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058589 restraints weight = 22578.850| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.45 r_work: 0.2785 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8584 Z= 0.245 Angle : 0.600 11.787 11777 Z= 0.314 Chirality : 0.042 0.173 1377 Planarity : 0.003 0.038 1358 Dihedral : 19.046 149.906 1496 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.66 % Allowed : 25.41 % Favored : 70.92 % 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: 2.16 (0.34), residues: 247 sheet: -0.65 (0.29), residues: 359 loop : -0.61 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 28 HIS 0.003 0.001 HIS C 44 PHE 0.008 0.001 PHE E 552 TYR 0.015 0.001 TYR B 249 ARG 0.006 0.000 ARG B 146 *********************** 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 122 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8763 (mp10) cc_final: 0.8392 (mp10) REVERT: B 40 MET cc_start: 0.7970 (ptm) cc_final: 0.6970 (ppp) REVERT: B 199 MET cc_start: 0.8555 (tpt) cc_final: 0.8133 (tpt) REVERT: C 28 TRP cc_start: 0.8988 (t-100) cc_final: 0.8782 (m100) REVERT: D 1 MET cc_start: 0.9028 (ppp) cc_final: 0.8010 (ppp) REVERT: D 119 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8036 (ptp) REVERT: E 488 ASN cc_start: 0.8814 (t0) cc_final: 0.8432 (t0) REVERT: E 545 PHE cc_start: 0.9121 (t80) cc_final: 0.8780 (t80) REVERT: E 552 PHE cc_start: 0.9109 (t80) cc_final: 0.8804 (t80) outliers start: 31 outliers final: 25 residues processed: 116 average time/residue: 0.2158 time to fit residues: 34.8963 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 88 ILE 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 139 MET 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 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 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: 0.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** E 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.093835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059433 restraints weight = 22204.796| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.63 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8584 Z= 0.158 Angle : 0.575 10.049 11777 Z= 0.302 Chirality : 0.041 0.180 1377 Planarity : 0.003 0.039 1358 Dihedral : 18.940 148.598 1496 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.60 % Allowed : 26.36 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.28), residues: 958 helix: 2.18 (0.33), residues: 249 sheet: -0.58 (0.29), residues: 359 loop : -0.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 28 HIS 0.002 0.000 HIS C 153 PHE 0.016 0.001 PHE E 407 TYR 0.012 0.001 TYR B 249 ARG 0.006 0.000 ARG B 146 ********************** 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 117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8553 (mp10) cc_final: 0.8145 (mp10) REVERT: B 40 MET cc_start: 0.7749 (ptm) cc_final: 0.6652 (ppp) REVERT: B 199 MET cc_start: 0.8622 (tpt) cc_final: 0.8256 (tpt) REVERT: C 28 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.6988 (m-90) REVERT: C 40 MET cc_start: 0.8091 (tpp) cc_final: 0.7788 (tpp) REVERT: D 1 MET cc_start: 0.8934 (ppp) cc_final: 0.7901 (ppp) REVERT: D 17 GLU cc_start: 0.9155 (tp30) cc_final: 0.8872 (tp30) REVERT: D 119 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7651 (ptp) REVERT: D 204 GLN cc_start: 0.9221 (tt0) cc_final: 0.8942 (mm-40) REVERT: E 488 ASN cc_start: 0.8700 (t0) cc_final: 0.8315 (t0) REVERT: E 545 PHE cc_start: 0.9057 (t80) cc_final: 0.8687 (t80) REVERT: E 547 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6114 (mtp180) REVERT: E 552 PHE cc_start: 0.9036 (t80) cc_final: 0.8706 (t80) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.2257 time to fit residues: 33.6014 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 : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 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 28 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 235 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.0050 chunk 29 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN E 490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.093900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059084 restraints weight = 22448.292| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.67 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8584 Z= 0.158 Angle : 0.592 12.089 11777 Z= 0.311 Chirality : 0.041 0.192 1377 Planarity : 0.003 0.039 1358 Dihedral : 18.889 148.084 1496 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 2.36 % Allowed : 26.83 % 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: 0.13 (0.28), residues: 958 helix: 2.18 (0.34), residues: 247 sheet: -0.52 (0.29), residues: 359 loop : -0.64 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 28 HIS 0.002 0.000 HIS C 153 PHE 0.012 0.001 PHE E 407 TYR 0.011 0.001 TYR B 249 ARG 0.006 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4603.59 seconds wall clock time: 82 minutes 22.76 seconds (4942.76 seconds total)