Starting phenix.real_space_refine on Sun Apr 5 06:05:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6n_72279/04_2026/9q6n_72279.map" } resolution = 2.8 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= 0.004 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5260 2.51 5 N 1440 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8399 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4643 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 24, 'TRANS': 559} Chain: "B" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "D" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 909 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Time building chain proxies: 2.14, per 1000 atoms: 0.25 Number of scatterers: 8399 At special positions: 0 Unit cell: (100.206, 110.754, 106.359, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1639 8.00 N 1440 7.00 C 5260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.04 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.04 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 118 " distance=2.04 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 118 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 112 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 111 " 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: 0.74 Conformation dependent library (CDL) restraints added in 346.2 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 48.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 59 through 80 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 143 through 170 removed outlier: 7.560A pdb=" N GLU A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 Processing helix chain 'A' and resid 197 through 230 removed outlier: 3.765A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 232 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 4.245A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 366 through 386 removed outlier: 4.143A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 399 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.257A pdb=" N LEU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.738A pdb=" N VAL A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 490 removed outlier: 4.257A pdb=" N MET A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix removed outlier: 4.090A pdb=" N LYS A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.042A pdb=" N SER A 504 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 527 through 531 removed outlier: 4.104A pdb=" N PHE A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.818A pdb=" N THR B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.709A pdb=" N SER B 133 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 123 through 127 removed outlier: 4.025A pdb=" N ILE D 127 " --> pdb=" O THR D 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.989A pdb=" N GLY B 32 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER B 149 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 34 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 115 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 71 " --> pdb=" O TRP B 58 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG B 60 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 69 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.559A pdb=" N SER B 93 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.143A pdb=" N GLY C 32 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER C 145 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 34 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 140 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 115 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 61 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET C 56 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR C 72 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP C 58 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.143A pdb=" N GLY C 32 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER C 145 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 34 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 140 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 37 removed outlier: 6.176A pdb=" N GLY D 33 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.616A pdb=" N VAL E 94 " --> pdb=" O CYS E 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.354A pdb=" N THR E 131 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 48 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA E 64 " --> pdb=" O TRP E 51 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER E 65 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR E 73 " --> pdb=" O SER E 65 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2791 1.35 - 1.47: 2075 1.47 - 1.59: 3624 1.59 - 1.72: 0 1.72 - 1.84: 75 Bond restraints: 8565 Sorted by residual: bond pdb=" N VAL D 109 " pdb=" CA VAL D 109 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" CA ALA D 108 " pdb=" C ALA D 108 " ideal model delta sigma weight residual 1.517 1.536 -0.018 6.30e-03 2.52e+04 8.55e+00 bond pdb=" N ARG A 233 " pdb=" CA ARG A 233 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.43e+00 bond pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.30e+00 bond pdb=" N TYR D 110 " pdb=" CA TYR D 110 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 ... (remaining 8560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11343 1.84 - 3.67: 196 3.67 - 5.51: 26 5.51 - 7.34: 1 7.34 - 9.18: 2 Bond angle restraints: 11568 Sorted by residual: angle pdb=" CA VAL D 109 " pdb=" C VAL D 109 " pdb=" O VAL D 109 " ideal model delta sigma weight residual 121.49 117.28 4.21 1.01e+00 9.80e-01 1.73e+01 angle pdb=" CA ALA D 108 " pdb=" C ALA D 108 " pdb=" O ALA D 108 " ideal model delta sigma weight residual 119.68 116.84 2.84 7.10e-01 1.98e+00 1.60e+01 angle pdb=" CA GLY A 423 " pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 122.37 119.88 2.49 7.30e-01 1.88e+00 1.16e+01 angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 111.48 108.44 3.04 9.40e-01 1.13e+00 1.04e+01 angle pdb=" CA GLY A 423 " pdb=" C GLY A 423 " pdb=" N GLU A 424 " ideal model delta sigma weight residual 114.13 117.69 -3.56 1.11e+00 8.12e-01 1.03e+01 ... (remaining 11563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4833 17.75 - 35.50: 329 35.50 - 53.25: 50 53.25 - 71.00: 11 71.00 - 88.75: 6 Dihedral angle restraints: 5229 sinusoidal: 2092 harmonic: 3137 Sorted by residual: dihedral pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual -86.00 -158.22 72.22 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CD ARG A 233 " pdb=" NE ARG A 233 " pdb=" CZ ARG A 233 " pdb=" NH1 ARG A 233 " ideal model delta sinusoidal sigma weight residual 0.00 -71.70 71.70 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual -86.00 -32.33 -53.67 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1143 0.070 - 0.139: 110 0.139 - 0.209: 2 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA SER D 139 " pdb=" N SER D 139 " pdb=" C SER D 139 " pdb=" CB SER D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB VAL D 109 " pdb=" CA VAL D 109 " pdb=" CG1 VAL D 109 " pdb=" CG2 VAL D 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1253 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 233 " 1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG A 233 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 233 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 233 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 233 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 189 " -0.015 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE A 189 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 189 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 189 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 189 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 189 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 189 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 111 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C SER D 111 " 0.031 2.00e-02 2.50e+03 pdb=" O SER D 111 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS D 112 " -0.011 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 113 2.45 - 3.07: 6445 3.07 - 3.68: 13143 3.68 - 4.29: 19640 4.29 - 4.90: 32524 Nonbonded interactions: 71865 Sorted by model distance: nonbonded pdb=" O ALA A 324 " pdb=" OG SER C 74 " model vdw 1.843 3.040 nonbonded pdb=" OG SER D 24 " pdb=" OG1 THR D 134 " model vdw 1.903 3.040 nonbonded pdb=" OG SER A 328 " pdb=" OD2 ASP C 132 " model vdw 1.964 3.040 nonbonded pdb=" OG SER C 29 " pdb=" O SER C 43 " model vdw 1.982 3.040 nonbonded pdb=" O ALA B 131 " pdb=" OH TYR B 137 " model vdw 2.025 3.040 ... (remaining 71860 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8587 Z= 0.203 Angle : 0.624 9.180 11612 Z= 0.359 Chirality : 0.041 0.348 1256 Planarity : 0.013 0.471 1510 Dihedral : 12.144 88.749 3149 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.50 % Favored : 88.66 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.26), residues: 1067 helix: 0.86 (0.24), residues: 439 sheet: -1.17 (0.45), residues: 128 loop : -2.00 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.021 0.002 TYR D 119 PHE 0.031 0.002 PHE A 189 TRP 0.008 0.001 TRP A 238 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8565) covalent geometry : angle 0.61782 (11568) SS BOND : bond 0.00487 ( 22) SS BOND : angle 1.59397 ( 44) hydrogen bonds : bond 0.18105 ( 425) hydrogen bonds : angle 7.41629 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.6597 (mt) cc_final: 0.6238 (mp) REVERT: A 396 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7793 (pmtt) REVERT: A 418 LEU cc_start: 0.8849 (tp) cc_final: 0.8424 (tp) REVERT: B 35 GLN cc_start: 0.7396 (tt0) cc_final: 0.6915 (mp10) REVERT: C 112 ASP cc_start: 0.7943 (m-30) cc_final: 0.7731 (m-30) REVERT: E 52 PHE cc_start: 0.7850 (m-80) cc_final: 0.7439 (m-10) outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.5991 time to fit residues: 157.4552 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 170 HIS A 194 GLN A 342 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.115189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.089992 restraints weight = 22354.405| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 4.44 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8587 Z= 0.209 Angle : 0.815 12.538 11612 Z= 0.421 Chirality : 0.047 0.219 1256 Planarity : 0.005 0.063 1510 Dihedral : 5.088 30.350 1182 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.06 % Favored : 91.19 % Rotamer: Outliers : 3.55 % Allowed : 15.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 1067 helix: 1.16 (0.24), residues: 433 sheet: -0.84 (0.45), residues: 126 loop : -1.86 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 78 TYR 0.030 0.002 TYR A 394 PHE 0.017 0.002 PHE A 235 TRP 0.010 0.002 TRP D 53 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8565) covalent geometry : angle 0.79666 (11568) SS BOND : bond 0.00586 ( 22) SS BOND : angle 2.89143 ( 44) hydrogen bonds : bond 0.05101 ( 425) hydrogen bonds : angle 5.81485 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.6953 (mt) cc_final: 0.6630 (mp) REVERT: A 197 ASP cc_start: 0.8572 (t70) cc_final: 0.8167 (t0) REVERT: A 233 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6855 (ttp80) REVERT: A 236 LYS cc_start: 0.6787 (mtpt) cc_final: 0.6062 (tmtt) REVERT: A 335 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7259 (mp0) REVERT: A 418 LEU cc_start: 0.8351 (tp) cc_final: 0.7887 (tp) REVERT: B 35 GLN cc_start: 0.7093 (tt0) cc_final: 0.6748 (mp10) REVERT: B 56 MET cc_start: 0.6387 (mpt) cc_final: 0.6173 (mpm) REVERT: C 24 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.6206 (p) REVERT: C 60 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7739 (mtp85) REVERT: C 95 ASP cc_start: 0.8316 (t0) cc_final: 0.8057 (t0) REVERT: C 102 TYR cc_start: 0.7155 (m-80) cc_final: 0.6935 (m-80) REVERT: D 60 MET cc_start: 0.8720 (ptt) cc_final: 0.8480 (pmt) REVERT: D 96 TYR cc_start: 0.8240 (m-80) cc_final: 0.7906 (m-80) REVERT: E 42 SER cc_start: 0.6336 (p) cc_final: 0.6087 (p) REVERT: E 51 TRP cc_start: 0.6717 (m100) cc_final: 0.6481 (m100) REVERT: E 52 PHE cc_start: 0.8603 (m-80) cc_final: 0.8048 (m-80) REVERT: E 60 ARG cc_start: 0.5932 (mtm180) cc_final: 0.5677 (mtp180) REVERT: E 97 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 110 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6574 (t80) outliers start: 32 outliers final: 7 residues processed: 199 average time/residue: 0.5571 time to fit residues: 118.3821 Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain E residue 110 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 15 optimal weight: 0.0770 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN D 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.116693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.091902 restraints weight = 22229.742| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 4.47 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8587 Z= 0.159 Angle : 0.765 12.807 11612 Z= 0.391 Chirality : 0.044 0.148 1256 Planarity : 0.005 0.043 1510 Dihedral : 4.928 30.939 1182 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.59 % Favored : 91.66 % Rotamer: Outliers : 3.88 % Allowed : 19.42 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1067 helix: 1.10 (0.24), residues: 435 sheet: -1.33 (0.40), residues: 150 loop : -1.85 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 79 TYR 0.028 0.002 TYR A 394 PHE 0.019 0.002 PHE A 531 TRP 0.006 0.001 TRP D 130 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8565) covalent geometry : angle 0.75091 (11568) SS BOND : bond 0.00480 ( 22) SS BOND : angle 2.47432 ( 44) hydrogen bonds : bond 0.04389 ( 425) hydrogen bonds : angle 5.38655 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.6907 (mt) cc_final: 0.6583 (mp) REVERT: A 197 ASP cc_start: 0.8667 (t70) cc_final: 0.8359 (t0) REVERT: A 236 LYS cc_start: 0.6726 (mtpt) cc_final: 0.5989 (tmtt) REVERT: A 332 ASP cc_start: 0.8536 (m-30) cc_final: 0.8121 (t0) REVERT: A 335 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7375 (mp0) REVERT: A 418 LEU cc_start: 0.8396 (tp) cc_final: 0.7959 (tp) REVERT: A 470 MET cc_start: 0.7107 (tmm) cc_final: 0.6182 (tpt) REVERT: B 35 GLN cc_start: 0.7567 (tt0) cc_final: 0.6937 (mp10) REVERT: B 56 MET cc_start: 0.6503 (mpt) cc_final: 0.6186 (mpm) REVERT: B 125 ASN cc_start: 0.8020 (t0) cc_final: 0.7805 (t0) REVERT: C 41 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7979 (mtp85) REVERT: C 60 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7982 (mtp85) REVERT: C 95 ASP cc_start: 0.8450 (t0) cc_final: 0.8125 (t0) REVERT: C 98 LYS cc_start: 0.8666 (tptp) cc_final: 0.8449 (tptp) REVERT: C 134 TYR cc_start: 0.7633 (m-10) cc_final: 0.6970 (m-80) REVERT: C 135 TYR cc_start: 0.8042 (m-80) cc_final: 0.7819 (m-80) REVERT: D 46 PHE cc_start: 0.8831 (m-80) cc_final: 0.8579 (m-80) REVERT: D 55 ARG cc_start: 0.6158 (mtt180) cc_final: 0.5036 (mmt180) REVERT: E 42 SER cc_start: 0.6622 (p) cc_final: 0.6385 (m) REVERT: E 44 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7447 (tmt170) REVERT: E 52 PHE cc_start: 0.8527 (m-80) cc_final: 0.7782 (m-10) REVERT: E 60 ARG cc_start: 0.5598 (mtm180) cc_final: 0.5363 (mtp180) REVERT: E 83 PHE cc_start: 0.7706 (m-10) cc_final: 0.7479 (m-80) REVERT: E 117 GLU cc_start: 0.7544 (tt0) cc_final: 0.6517 (tm-30) REVERT: E 121 TYR cc_start: 0.7331 (m-80) cc_final: 0.6366 (m-80) outliers start: 35 outliers final: 16 residues processed: 182 average time/residue: 0.5645 time to fit residues: 109.4670 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN D 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.115426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.090218 restraints weight = 22851.857| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 4.59 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8587 Z= 0.173 Angle : 0.800 13.268 11612 Z= 0.404 Chirality : 0.046 0.311 1256 Planarity : 0.005 0.042 1510 Dihedral : 5.096 39.432 1182 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.69 % Favored : 91.57 % Rotamer: Outliers : 5.22 % Allowed : 20.09 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.26), residues: 1067 helix: 1.15 (0.24), residues: 430 sheet: -1.21 (0.40), residues: 151 loop : -1.90 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 79 TYR 0.027 0.002 TYR A 394 PHE 0.018 0.002 PHE A 235 TRP 0.009 0.001 TRP D 53 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8565) covalent geometry : angle 0.78691 (11568) SS BOND : bond 0.00555 ( 22) SS BOND : angle 2.45337 ( 44) hydrogen bonds : bond 0.04702 ( 425) hydrogen bonds : angle 5.28733 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.6979 (mt) cc_final: 0.6613 (mp) REVERT: A 197 ASP cc_start: 0.8669 (t70) cc_final: 0.8336 (t0) REVERT: A 236 LYS cc_start: 0.6735 (mtpt) cc_final: 0.5994 (tmtt) REVERT: A 242 ARG cc_start: 0.6774 (tpt170) cc_final: 0.6453 (tpm-80) REVERT: A 332 ASP cc_start: 0.8494 (m-30) cc_final: 0.8056 (t0) REVERT: A 335 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7364 (mp0) REVERT: A 418 LEU cc_start: 0.8419 (tp) cc_final: 0.7966 (tp) REVERT: A 470 MET cc_start: 0.7039 (tmm) cc_final: 0.6158 (tpt) REVERT: B 35 GLN cc_start: 0.7705 (tt0) cc_final: 0.7043 (mp10) REVERT: B 56 MET cc_start: 0.6643 (mpt) cc_final: 0.6242 (mpm) REVERT: B 104 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6761 (tm-30) REVERT: B 125 ASN cc_start: 0.8014 (t0) cc_final: 0.7668 (t0) REVERT: B 132 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7471 (mtp180) REVERT: C 41 ARG cc_start: 0.8481 (mtp85) cc_final: 0.7901 (mtp85) REVERT: C 60 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7826 (mtp85) REVERT: C 109 LYS cc_start: 0.8844 (pttm) cc_final: 0.8099 (pmtt) REVERT: C 135 TYR cc_start: 0.8153 (m-80) cc_final: 0.7951 (m-80) REVERT: D 46 PHE cc_start: 0.8893 (m-80) cc_final: 0.8681 (m-80) REVERT: D 61 GLU cc_start: 0.7041 (tp30) cc_final: 0.6796 (tp30) REVERT: D 63 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 96 TYR cc_start: 0.8157 (m-80) cc_final: 0.7814 (m-80) REVERT: E 42 SER cc_start: 0.6469 (p) cc_final: 0.6249 (m) REVERT: E 44 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7434 (tmt-80) REVERT: E 52 PHE cc_start: 0.8593 (m-80) cc_final: 0.7865 (m-80) REVERT: E 83 PHE cc_start: 0.7690 (m-10) cc_final: 0.7471 (m-80) REVERT: E 110 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6161 (t80) outliers start: 47 outliers final: 21 residues processed: 176 average time/residue: 0.5902 time to fit residues: 110.3986 Evaluate side-chains 147 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 63 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.112892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.087764 restraints weight = 22650.699| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 4.50 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8587 Z= 0.205 Angle : 0.788 13.443 11612 Z= 0.403 Chirality : 0.046 0.198 1256 Planarity : 0.005 0.048 1510 Dihedral : 5.094 29.300 1182 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.78 % Favored : 91.38 % Rotamer: Outliers : 6.33 % Allowed : 20.31 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1067 helix: 1.11 (0.24), residues: 431 sheet: -1.22 (0.41), residues: 139 loop : -1.91 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 78 TYR 0.028 0.002 TYR C 133 PHE 0.021 0.002 PHE A 235 TRP 0.007 0.002 TRP E 68 HIS 0.002 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8565) covalent geometry : angle 0.77172 (11568) SS BOND : bond 0.00739 ( 22) SS BOND : angle 2.68308 ( 44) hydrogen bonds : bond 0.04799 ( 425) hydrogen bonds : angle 5.26504 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8670 (t70) cc_final: 0.8321 (t0) REVERT: A 236 LYS cc_start: 0.6850 (mtpt) cc_final: 0.6139 (tmtt) REVERT: A 335 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7851 (mp0) REVERT: A 418 LEU cc_start: 0.8397 (tp) cc_final: 0.8126 (tp) REVERT: A 470 MET cc_start: 0.7087 (tmm) cc_final: 0.6277 (tpt) REVERT: A 589 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 35 GLN cc_start: 0.7720 (tt0) cc_final: 0.7079 (mp10) REVERT: B 104 GLN cc_start: 0.7293 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 125 ASN cc_start: 0.8032 (t0) cc_final: 0.7659 (t0) REVERT: C 41 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7862 (mtp85) REVERT: C 135 TYR cc_start: 0.8210 (m-80) cc_final: 0.7969 (m-80) REVERT: D 97 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8529 (mm) REVERT: E 42 SER cc_start: 0.6222 (p) cc_final: 0.5996 (m) REVERT: E 44 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7387 (tmt-80) REVERT: E 49 MET cc_start: 0.6364 (mmm) cc_final: 0.6155 (mmt) REVERT: E 52 PHE cc_start: 0.8573 (m-80) cc_final: 0.8022 (m-80) REVERT: E 110 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6988 (t80) outliers start: 57 outliers final: 32 residues processed: 165 average time/residue: 0.5737 time to fit residues: 100.7594 Evaluate side-chains 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN E 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.114965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.089875 restraints weight = 22269.980| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 4.50 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8587 Z= 0.162 Angle : 0.773 13.386 11612 Z= 0.391 Chirality : 0.044 0.205 1256 Planarity : 0.004 0.048 1510 Dihedral : 5.054 29.542 1182 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.22 % Favored : 92.03 % Rotamer: Outliers : 5.88 % Allowed : 22.53 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 1067 helix: 1.18 (0.24), residues: 432 sheet: -1.31 (0.40), residues: 144 loop : -1.82 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 78 TYR 0.026 0.002 TYR A 394 PHE 0.019 0.002 PHE A 235 TRP 0.008 0.001 TRP E 51 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8565) covalent geometry : angle 0.76647 (11568) SS BOND : bond 0.00447 ( 22) SS BOND : angle 1.76561 ( 44) hydrogen bonds : bond 0.04250 ( 425) hydrogen bonds : angle 5.06290 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.5234 (OUTLIER) cc_final: 0.4330 (t80) REVERT: A 197 ASP cc_start: 0.8644 (t70) cc_final: 0.8275 (t0) REVERT: A 236 LYS cc_start: 0.6719 (mtpt) cc_final: 0.6032 (tmtt) REVERT: A 335 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7994 (mp0) REVERT: A 418 LEU cc_start: 0.8379 (tp) cc_final: 0.8103 (tp) REVERT: A 470 MET cc_start: 0.7021 (tmm) cc_final: 0.6171 (tpt) REVERT: A 589 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 35 GLN cc_start: 0.7707 (tt0) cc_final: 0.7115 (mp10) REVERT: B 56 MET cc_start: 0.6668 (mpt) cc_final: 0.6180 (mpm) REVERT: B 104 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6861 (tm-30) REVERT: B 125 ASN cc_start: 0.7972 (t0) cc_final: 0.7526 (t0) REVERT: C 41 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8330 (mtp85) REVERT: C 60 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7475 (mmm-85) REVERT: C 102 TYR cc_start: 0.7153 (m-80) cc_final: 0.6826 (m-80) REVERT: C 109 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7913 (pptt) REVERT: D 46 PHE cc_start: 0.8764 (m-80) cc_final: 0.8536 (m-80) REVERT: D 54 PHE cc_start: 0.7543 (m-10) cc_final: 0.7308 (m-10) REVERT: E 42 SER cc_start: 0.5992 (p) cc_final: 0.5720 (m) REVERT: E 44 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7388 (tmt170) REVERT: E 49 MET cc_start: 0.6355 (mmm) cc_final: 0.6151 (mmt) REVERT: E 52 PHE cc_start: 0.8558 (m-80) cc_final: 0.7959 (m-80) outliers start: 53 outliers final: 24 residues processed: 175 average time/residue: 0.5240 time to fit residues: 98.2205 Evaluate side-chains 148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.113352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.088035 restraints weight = 22768.598| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.54 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8587 Z= 0.203 Angle : 0.843 16.525 11612 Z= 0.428 Chirality : 0.047 0.304 1256 Planarity : 0.005 0.051 1510 Dihedral : 5.291 40.949 1182 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.34 % Favored : 90.82 % Rotamer: Outliers : 5.11 % Allowed : 23.97 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.26), residues: 1067 helix: 1.03 (0.24), residues: 435 sheet: -1.64 (0.39), residues: 143 loop : -1.82 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 78 TYR 0.041 0.002 TYR D 110 PHE 0.022 0.002 PHE A 235 TRP 0.014 0.002 TRP E 51 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8565) covalent geometry : angle 0.81329 (11568) SS BOND : bond 0.00601 ( 22) SS BOND : angle 3.68583 ( 44) hydrogen bonds : bond 0.04808 ( 425) hydrogen bonds : angle 5.18247 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 HIS cc_start: 0.7175 (m-70) cc_final: 0.6668 (m170) REVERT: A 197 ASP cc_start: 0.8669 (t70) cc_final: 0.8328 (t0) REVERT: A 236 LYS cc_start: 0.6848 (mtpt) cc_final: 0.6140 (tmtt) REVERT: A 335 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8055 (mp0) REVERT: A 418 LEU cc_start: 0.8407 (tp) cc_final: 0.8143 (tp) REVERT: A 469 ARG cc_start: 0.6885 (tpp-160) cc_final: 0.6540 (tpt170) REVERT: A 470 MET cc_start: 0.6970 (tmm) cc_final: 0.6144 (tpt) REVERT: A 472 CYS cc_start: 0.5581 (m) cc_final: 0.5075 (t) REVERT: A 589 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: B 35 GLN cc_start: 0.7707 (tt0) cc_final: 0.7142 (mp10) REVERT: B 104 GLN cc_start: 0.7296 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 125 ASN cc_start: 0.8029 (t0) cc_final: 0.7576 (t0) REVERT: C 41 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8281 (mtp85) REVERT: C 109 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7976 (pptt) REVERT: C 135 TYR cc_start: 0.8212 (m-80) cc_final: 0.7966 (m-80) REVERT: D 54 PHE cc_start: 0.7496 (m-10) cc_final: 0.7068 (m-10) REVERT: E 42 SER cc_start: 0.6149 (p) cc_final: 0.5892 (m) REVERT: E 44 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7406 (tmt170) REVERT: E 52 PHE cc_start: 0.8604 (m-80) cc_final: 0.8114 (m-80) REVERT: E 83 PHE cc_start: 0.7732 (m-10) cc_final: 0.7390 (m-10) REVERT: E 98 MET cc_start: 0.7011 (mmt) cc_final: 0.6596 (mmt) outliers start: 46 outliers final: 25 residues processed: 160 average time/residue: 0.5829 time to fit residues: 99.3757 Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.114467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.089473 restraints weight = 22236.992| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 4.50 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8587 Z= 0.167 Angle : 0.794 13.554 11612 Z= 0.399 Chirality : 0.044 0.176 1256 Planarity : 0.004 0.045 1510 Dihedral : 5.111 30.982 1182 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.69 % Favored : 91.66 % Rotamer: Outliers : 4.33 % Allowed : 25.64 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.26), residues: 1067 helix: 1.03 (0.24), residues: 437 sheet: -1.62 (0.40), residues: 143 loop : -1.83 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 78 TYR 0.026 0.002 TYR D 110 PHE 0.021 0.002 PHE A 235 TRP 0.009 0.001 TRP E 51 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8565) covalent geometry : angle 0.78329 (11568) SS BOND : bond 0.00671 ( 22) SS BOND : angle 2.22753 ( 44) hydrogen bonds : bond 0.04340 ( 425) hydrogen bonds : angle 5.02258 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.4417 (t80) REVERT: A 197 ASP cc_start: 0.8654 (t70) cc_final: 0.8344 (t0) REVERT: A 236 LYS cc_start: 0.6781 (mtpt) cc_final: 0.6073 (tmtt) REVERT: A 335 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8008 (mp0) REVERT: A 418 LEU cc_start: 0.8399 (tp) cc_final: 0.8116 (tp) REVERT: A 469 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6140 (tpt170) REVERT: A 470 MET cc_start: 0.7232 (tmm) cc_final: 0.6297 (tpt) REVERT: A 589 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 35 GLN cc_start: 0.7745 (tt0) cc_final: 0.7186 (mp10) REVERT: B 104 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 125 ASN cc_start: 0.8022 (t0) cc_final: 0.7567 (t0) REVERT: C 109 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7982 (pptt) REVERT: C 135 TYR cc_start: 0.8206 (m-80) cc_final: 0.7904 (m-80) REVERT: D 46 PHE cc_start: 0.8576 (m-80) cc_final: 0.8314 (m-80) REVERT: D 60 MET cc_start: 0.8151 (pp-130) cc_final: 0.7932 (ppp) REVERT: D 69 ARG cc_start: 0.7622 (mpt-90) cc_final: 0.7060 (mpt-90) REVERT: E 44 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7353 (tmt170) REVERT: E 52 PHE cc_start: 0.8568 (m-80) cc_final: 0.7888 (m-80) outliers start: 39 outliers final: 25 residues processed: 156 average time/residue: 0.6130 time to fit residues: 101.6724 Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 292 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.116599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.091743 restraints weight = 22708.308| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 4.60 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8587 Z= 0.153 Angle : 0.816 13.387 11612 Z= 0.414 Chirality : 0.044 0.180 1256 Planarity : 0.004 0.041 1510 Dihedral : 5.098 32.338 1182 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.97 % Favored : 91.38 % Rotamer: Outliers : 3.33 % Allowed : 27.30 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.26), residues: 1067 helix: 1.07 (0.24), residues: 437 sheet: -1.63 (0.40), residues: 142 loop : -1.88 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 41 TYR 0.026 0.002 TYR A 394 PHE 0.023 0.002 PHE A 247 TRP 0.008 0.001 TRP E 124 HIS 0.009 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8565) covalent geometry : angle 0.80729 (11568) SS BOND : bond 0.00382 ( 22) SS BOND : angle 2.04823 ( 44) hydrogen bonds : bond 0.04152 ( 425) hydrogen bonds : angle 4.95224 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8724 (t70) cc_final: 0.8421 (t0) REVERT: A 236 LYS cc_start: 0.6757 (mtpt) cc_final: 0.6038 (tmtt) REVERT: A 332 ASP cc_start: 0.8389 (m-30) cc_final: 0.8004 (t0) REVERT: A 335 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8156 (mp0) REVERT: A 418 LEU cc_start: 0.8378 (tp) cc_final: 0.8085 (tp) REVERT: A 469 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6578 (tpt170) REVERT: A 470 MET cc_start: 0.6826 (tmm) cc_final: 0.6046 (tpt) REVERT: A 589 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: B 35 GLN cc_start: 0.7837 (tt0) cc_final: 0.7247 (mp10) REVERT: B 104 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6942 (tm-30) REVERT: B 125 ASN cc_start: 0.7983 (t0) cc_final: 0.7497 (t0) REVERT: C 135 TYR cc_start: 0.8211 (m-80) cc_final: 0.7907 (m-80) REVERT: E 44 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7078 (tmt90) REVERT: E 52 PHE cc_start: 0.8473 (m-80) cc_final: 0.7767 (m-80) REVERT: E 110 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 30 outliers final: 21 residues processed: 150 average time/residue: 0.5942 time to fit residues: 94.7419 Evaluate side-chains 139 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.091223 restraints weight = 22866.537| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 4.59 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8587 Z= 0.169 Angle : 0.874 13.732 11612 Z= 0.443 Chirality : 0.046 0.309 1256 Planarity : 0.005 0.069 1510 Dihedral : 5.293 41.087 1182 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.59 % Favored : 91.66 % Rotamer: Outliers : 3.00 % Allowed : 27.97 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.26), residues: 1067 helix: 1.00 (0.25), residues: 434 sheet: -1.53 (0.40), residues: 147 loop : -1.90 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 78 TYR 0.026 0.002 TYR A 394 PHE 0.033 0.002 PHE A 575 TRP 0.016 0.002 TRP E 51 HIS 0.011 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8565) covalent geometry : angle 0.85880 (11568) SS BOND : bond 0.00417 ( 22) SS BOND : angle 2.75370 ( 44) hydrogen bonds : bond 0.04492 ( 425) hydrogen bonds : angle 5.01230 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8712 (t70) cc_final: 0.8412 (t0) REVERT: A 236 LYS cc_start: 0.6819 (mtpt) cc_final: 0.6110 (tmtt) REVERT: A 332 ASP cc_start: 0.8369 (m-30) cc_final: 0.8006 (t0) REVERT: A 335 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8226 (mp0) REVERT: A 418 LEU cc_start: 0.8407 (tp) cc_final: 0.8113 (tp) REVERT: A 470 MET cc_start: 0.6956 (tmm) cc_final: 0.6169 (tpt) REVERT: A 589 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: B 35 GLN cc_start: 0.7825 (tt0) cc_final: 0.7239 (mp10) REVERT: B 104 GLN cc_start: 0.7345 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 125 ASN cc_start: 0.8026 (t0) cc_final: 0.7541 (t0) REVERT: C 135 TYR cc_start: 0.8230 (m-80) cc_final: 0.7885 (m-80) REVERT: D 46 PHE cc_start: 0.8606 (m-80) cc_final: 0.8101 (m-80) REVERT: E 44 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7096 (tmt90) REVERT: E 52 PHE cc_start: 0.8483 (m-80) cc_final: 0.7777 (m-80) REVERT: E 110 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6526 (t80) outliers start: 27 outliers final: 20 residues processed: 142 average time/residue: 0.5379 time to fit residues: 81.6771 Evaluate side-chains 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** 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 = 0.4414 r_free = 0.4414 target = 0.116743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.092096 restraints weight = 22765.358| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 4.57 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8587 Z= 0.168 Angle : 0.877 15.185 11612 Z= 0.446 Chirality : 0.045 0.238 1256 Planarity : 0.005 0.086 1510 Dihedral : 5.188 34.051 1182 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.50 % Favored : 91.75 % Rotamer: Outliers : 3.33 % Allowed : 27.97 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.26), residues: 1067 helix: 0.96 (0.25), residues: 437 sheet: -1.53 (0.40), residues: 148 loop : -1.91 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 78 TYR 0.026 0.002 TYR A 394 PHE 0.054 0.002 PHE A 575 TRP 0.023 0.002 TRP E 51 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8565) covalent geometry : angle 0.87004 (11568) SS BOND : bond 0.00470 ( 22) SS BOND : angle 1.98490 ( 44) hydrogen bonds : bond 0.04270 ( 425) hydrogen bonds : angle 5.05272 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.39 seconds wall clock time: 56 minutes 35.45 seconds (3395.45 seconds total)