Starting phenix.real_space_refine on Fri Jul 3 03:22:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.cif Found real_map, /net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.map" model { file = "/net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26lk_80744/07_2026/26lk_80744.cif" } resolution = 3.4 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= 0.003 sd= 0.076 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 72 5.16 5 C 7360 2.51 5 N 1990 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11504 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1623 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1623 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4129 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4129 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 481} Chain breaks: 2 Time building chain proxies: 2.25, per 1000 atoms: 0.20 Number of scatterers: 11504 At special positions: 0 Unit cell: (191.06, 81.084, 84.812, 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 72 16.00 O 2082 8.00 N 1990 7.00 C 7360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.85 Conformation dependent library (CDL) restraints added in 307.8 milliseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 40.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.793A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 removed outlier: 3.605A pdb=" N ILE A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.933A pdb=" N SER A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.719A pdb=" N LEU A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.309A pdb=" N VAL A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.561A pdb=" N GLN B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 103 removed outlier: 3.770A pdb=" N ARG B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.940A pdb=" N LEU B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 119 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 removed outlier: 4.156A pdb=" N VAL B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 620 through 631 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 229 through 238 removed outlier: 3.644A pdb=" N TYR C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.526A pdb=" N GLU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 Processing helix chain 'C' and resid 311 through 325 removed outlier: 3.563A pdb=" N PHE C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 412 through 427 removed outlier: 3.561A pdb=" N LEU C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 453 Processing helix chain 'C' and resid 509 through 528 removed outlier: 3.735A pdb=" N GLU C 513 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 514 " --> pdb=" O ARG C 510 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 532 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 628 through 633 Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.720A pdb=" N LEU C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 229 through 238 removed outlier: 3.616A pdb=" N TYR D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 278 through 294 Processing helix chain 'D' and resid 295 through 298 Processing helix chain 'D' and resid 311 through 325 Processing helix chain 'D' and resid 382 through 396 removed outlier: 3.899A pdb=" N TYR D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 removed outlier: 3.656A pdb=" N LEU D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 453 Processing helix chain 'D' and resid 509 through 528 removed outlier: 3.607A pdb=" N GLU D 513 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 628 through 633 removed outlier: 3.535A pdb=" N LEU D 632 " --> pdb=" O PRO D 628 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 633 " --> pdb=" O PRO D 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 628 through 633' Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.672A pdb=" N LEU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 639 through 640 removed outlier: 3.821A pdb=" N ILE C 623 " --> pdb=" O TYR C 548 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 620 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE C 614 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N HIS C 622 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 637 " --> pdb=" O CYS C 581 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA C 556 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 640 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG C 558 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 671 through 673 removed outlier: 6.219A pdb=" N ASP A 671 " --> pdb=" O LEU C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 639 through 640 removed outlier: 3.805A pdb=" N ILE D 623 " --> pdb=" O TYR D 548 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 613 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU D 624 " --> pdb=" O CYS D 611 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N CYS D 611 " --> pdb=" O LEU D 624 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA D 556 " --> pdb=" O LEU D 638 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL D 640 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG D 558 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 557 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 671 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.233A pdb=" N ILE C 221 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 157 Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.929A pdb=" N ASP C 331 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN C 406 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 333 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 302 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 430 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 347 through 348 Processing sheet with id=AA8, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AA9, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.749A pdb=" N LEU D 223 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS D 144 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU D 225 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL D 142 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 154 through 157 removed outlier: 3.576A pdb=" N HIS D 177 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 372 through 373 removed outlier: 3.611A pdb=" N VAL D 372 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS D 430 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 434 through 435 456 hydrogen bonds defined for protein. 1290 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: 1.69 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1850 1.32 - 1.44: 3124 1.44 - 1.57: 6704 1.57 - 1.70: 6 1.70 - 1.83: 96 Bond restraints: 11780 Sorted by residual: bond pdb=" C ARG A 79 " pdb=" O ARG A 79 " ideal model delta sigma weight residual 1.236 1.188 0.047 1.32e-02 5.74e+03 1.29e+01 bond pdb=" C ARG A 654 " pdb=" N MET A 655 " ideal model delta sigma weight residual 1.323 1.268 0.055 1.64e-02 3.72e+03 1.12e+01 bond pdb=" N LYS B 161 " pdb=" CA LYS B 161 " ideal model delta sigma weight residual 1.460 1.487 -0.027 8.20e-03 1.49e+04 1.09e+01 bond pdb=" N VAL B 120 " pdb=" CA VAL B 120 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.40e+00 ... (remaining 11775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 15768 3.77 - 7.55: 217 7.55 - 11.32: 25 11.32 - 15.09: 13 15.09 - 18.87: 1 Bond angle restraints: 16024 Sorted by residual: angle pdb=" CA PRO A 651 " pdb=" N PRO A 651 " pdb=" CD PRO A 651 " ideal model delta sigma weight residual 112.00 99.85 12.15 1.40e+00 5.10e-01 7.53e+01 angle pdb=" CA PRO B 651 " pdb=" N PRO B 651 " pdb=" CD PRO B 651 " ideal model delta sigma weight residual 112.00 100.10 11.90 1.40e+00 5.10e-01 7.22e+01 angle pdb=" CA PRO D 402 " pdb=" N PRO D 402 " pdb=" CD PRO D 402 " ideal model delta sigma weight residual 112.00 100.52 11.48 1.40e+00 5.10e-01 6.73e+01 angle pdb=" CA PRO D 361 " pdb=" N PRO D 361 " pdb=" CD PRO D 361 " ideal model delta sigma weight residual 112.00 101.05 10.95 1.40e+00 5.10e-01 6.12e+01 angle pdb=" CA PRO C 361 " pdb=" N PRO C 361 " pdb=" CD PRO C 361 " ideal model delta sigma weight residual 112.00 101.32 10.68 1.40e+00 5.10e-01 5.82e+01 ... (remaining 16019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5902 17.98 - 35.96: 877 35.96 - 53.94: 239 53.94 - 71.92: 67 71.92 - 89.90: 23 Dihedral angle restraints: 7108 sinusoidal: 2894 harmonic: 4214 Sorted by residual: dihedral pdb=" CA PRO C 538 " pdb=" C PRO C 538 " pdb=" N LEU C 539 " pdb=" CA LEU C 539 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG C 512 " pdb=" C ARG C 512 " pdb=" N GLU C 513 " pdb=" CA GLU C 513 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN C 511 " pdb=" C ASN C 511 " pdb=" N ARG C 512 " pdb=" CA ARG C 512 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 7105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1669 0.101 - 0.203: 137 0.203 - 0.304: 12 0.304 - 0.406: 3 0.406 - 0.507: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CG LEU D 418 " pdb=" CB LEU D 418 " pdb=" CD1 LEU D 418 " pdb=" CD2 LEU D 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CG LEU C 539 " pdb=" CB LEU C 539 " pdb=" CD1 LEU C 539 " pdb=" CD2 LEU C 539 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CG LEU C 418 " pdb=" CB LEU C 418 " pdb=" CD1 LEU C 418 " pdb=" CD2 LEU C 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 1819 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 650 " -0.125 5.00e-02 4.00e+02 1.79e-01 5.13e+01 pdb=" N PRO A 651 " 0.309 5.00e-02 4.00e+02 pdb=" CA PRO A 651 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO A 651 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 650 " 0.122 5.00e-02 4.00e+02 1.75e-01 4.87e+01 pdb=" N PRO B 651 " -0.301 5.00e-02 4.00e+02 pdb=" CA PRO B 651 " 0.097 5.00e-02 4.00e+02 pdb=" CD PRO B 651 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 625 " -0.094 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO D 626 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO D 626 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO D 626 " -0.071 5.00e-02 4.00e+02 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2093 2.77 - 3.31: 10535 3.31 - 3.84: 19388 3.84 - 4.37: 21901 4.37 - 4.90: 37333 Nonbonded interactions: 91250 Sorted by model distance: nonbonded pdb=" OD1 ASP C 331 " pdb=" OG SER C 401 " model vdw 2.243 3.040 nonbonded pdb=" O TRP B 179 " pdb=" OG1 THR B 183 " model vdw 2.249 3.040 nonbonded pdb=" O TRP A 179 " pdb=" OG1 THR A 183 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR C 397 " pdb=" O SER C 401 " model vdw 2.269 3.040 nonbonded pdb=" O ASP C 207 " pdb=" OG SER C 211 " model vdw 2.270 3.040 ... (remaining 91245 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 : 0.006 0.098 11780 Z= 0.300 Angle : 1.162 18.867 16024 Z= 0.642 Chirality : 0.061 0.507 1822 Planarity : 0.013 0.179 2040 Dihedral : 19.175 89.895 4388 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.79 % Rotamer: Outliers : 1.69 % Allowed : 32.46 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.90 (0.21), residues: 1420 helix: -0.19 (0.21), residues: 520 sheet: -2.51 (0.35), residues: 182 loop : -1.71 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 96 TYR 0.066 0.003 TYR C 662 PHE 0.048 0.003 PHE C 215 TRP 0.059 0.003 TRP C 410 HIS 0.007 0.001 HIS C 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.30 (11780) covalent geometry : angle 1.16161 / 0.64 (16024) hydrogen bonds : bond 0.17683 / 11.90 ( 456) hydrogen bonds : angle 7.15334 / 5.12 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 163 MET cc_start: 0.7788 (tpp) cc_final: 0.7569 (mmt) REVERT: A 630 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7311 (mtt90) REVERT: A 655 MET cc_start: 0.7245 (mmt) cc_final: 0.7028 (tpt) REVERT: B 112 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7290 (mtm180) REVERT: B 119 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7530 (mm) REVERT: B 630 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7156 (mtt90) REVERT: C 136 PHE cc_start: 0.6960 (p90) cc_final: 0.6482 (p90) REVERT: C 370 LYS cc_start: 0.7300 (tppt) cc_final: 0.7087 (tppp) REVERT: D 157 SER cc_start: 0.8519 (m) cc_final: 0.7870 (t) REVERT: D 158 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: D 160 GLN cc_start: 0.7918 (mp10) cc_final: 0.6959 (mp10) REVERT: D 391 LYS cc_start: 0.7474 (ttmt) cc_final: 0.7193 (mmmt) REVERT: D 571 TYR cc_start: 0.8086 (m-80) cc_final: 0.7658 (m-80) outliers start: 22 outliers final: 4 residues processed: 302 average time/residue: 0.1063 time to fit residues: 44.7591 Evaluate side-chains 207 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN C 148 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN C 599 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163802 restraints weight = 12427.306| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.53 r_work: 0.3365 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11780 Z= 0.190 Angle : 0.701 9.725 16024 Z= 0.347 Chirality : 0.046 0.193 1822 Planarity : 0.008 0.100 2040 Dihedral : 6.131 56.591 1597 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 5.23 % Allowed : 25.77 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.13 (0.22), residues: 1420 helix: 0.90 (0.22), residues: 524 sheet: -1.98 (0.35), residues: 208 loop : -1.66 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 588 TYR 0.019 0.002 TYR C 571 PHE 0.019 0.002 PHE C 362 TRP 0.023 0.002 TRP C 210 HIS 0.005 0.001 HIS C 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (11780) covalent geometry : angle 0.70081 / 0.35 (16024) hydrogen bonds : bond 0.04375 / 2.78 ( 456) hydrogen bonds : angle 5.27029 / 3.74 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: A 630 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7804 (mtt90) REVERT: B 119 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 157 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 630 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7679 (mtt90) REVERT: C 160 GLN cc_start: 0.7871 (mp10) cc_final: 0.7642 (mp10) REVERT: C 168 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 198 LEU cc_start: 0.9078 (mm) cc_final: 0.8849 (mm) REVERT: C 269 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: D 136 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6623 (p90) REVERT: D 157 SER cc_start: 0.8633 (m) cc_final: 0.8042 (t) REVERT: D 158 GLN cc_start: 0.7835 (tt0) cc_final: 0.7290 (pm20) REVERT: D 160 GLN cc_start: 0.8263 (mp10) cc_final: 0.7098 (mp10) REVERT: D 198 LEU cc_start: 0.9091 (mm) cc_final: 0.8884 (mm) REVERT: D 384 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: D 571 TYR cc_start: 0.8478 (m-80) cc_final: 0.8078 (m-80) outliers start: 68 outliers final: 28 residues processed: 260 average time/residue: 0.0877 time to fit residues: 33.8638 Evaluate side-chains 223 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 664 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.205770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164807 restraints weight = 12589.711| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.43 r_work: 0.3401 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11780 Z= 0.158 Angle : 0.653 10.635 16024 Z= 0.317 Chirality : 0.044 0.275 1822 Planarity : 0.006 0.071 2040 Dihedral : 4.865 53.307 1584 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 4.54 % Allowed : 25.15 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.94 (0.22), residues: 1420 helix: 1.08 (0.22), residues: 536 sheet: -2.01 (0.36), residues: 196 loop : -1.60 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 193 TYR 0.016 0.001 TYR C 571 PHE 0.015 0.002 PHE C 362 TRP 0.023 0.002 TRP C 210 HIS 0.004 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11780) covalent geometry : angle 0.65259 / 0.32 (16024) hydrogen bonds : bond 0.04008 / 2.55 ( 456) hydrogen bonds : angle 4.98060 / 3.53 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7891 (pttm) REVERT: A 157 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 630 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7807 (mtt90) REVERT: B 64 LYS cc_start: 0.8453 (pttp) cc_final: 0.7907 (ptpp) REVERT: B 119 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8165 (mm) REVERT: B 157 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7758 (mt-10) REVERT: C 158 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: C 160 GLN cc_start: 0.7940 (mp10) cc_final: 0.7310 (mp10) REVERT: C 198 LEU cc_start: 0.9056 (mm) cc_final: 0.8776 (mm) REVERT: C 287 GLU cc_start: 0.8215 (pt0) cc_final: 0.7937 (pt0) REVERT: C 318 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: D 158 GLN cc_start: 0.7928 (tt0) cc_final: 0.7595 (pm20) REVERT: D 496 LEU cc_start: 0.8172 (tt) cc_final: 0.7446 (mt) REVERT: D 571 TYR cc_start: 0.8449 (m-80) cc_final: 0.8014 (m-80) REVERT: D 612 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7808 (ttm-80) outliers start: 59 outliers final: 31 residues processed: 239 average time/residue: 0.0908 time to fit residues: 31.7868 Evaluate side-chains 207 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.207805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166272 restraints weight = 12605.665| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.50 r_work: 0.3399 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11780 Z= 0.125 Angle : 0.619 9.013 16024 Z= 0.299 Chirality : 0.043 0.296 1822 Planarity : 0.006 0.059 2040 Dihedral : 4.697 53.871 1584 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 3.38 % Allowed : 26.77 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.63 (0.22), residues: 1420 helix: 1.42 (0.22), residues: 536 sheet: -1.94 (0.36), residues: 196 loop : -1.46 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 588 TYR 0.014 0.001 TYR A 184 PHE 0.018 0.002 PHE C 134 TRP 0.036 0.001 TRP C 210 HIS 0.003 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11780) covalent geometry : angle 0.61880 / 0.30 (16024) hydrogen bonds : bond 0.03489 / 2.21 ( 456) hydrogen bonds : angle 4.72779 / 3.35 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 630 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7788 (mtt90) REVERT: B 64 LYS cc_start: 0.8453 (pttp) cc_final: 0.7883 (ptpp) REVERT: B 119 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8156 (mm) REVERT: B 157 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 198 LEU cc_start: 0.9080 (mm) cc_final: 0.8827 (mm) REVERT: C 308 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7489 (mp10) REVERT: C 318 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: C 421 ASP cc_start: 0.7104 (m-30) cc_final: 0.6790 (m-30) REVERT: D 136 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6935 (p90) REVERT: D 158 GLN cc_start: 0.8168 (tt0) cc_final: 0.7731 (pm20) REVERT: D 202 HIS cc_start: 0.7575 (t-90) cc_final: 0.7216 (t-90) REVERT: D 270 LYS cc_start: 0.8582 (ptmm) cc_final: 0.8304 (ptmm) REVERT: D 384 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: D 408 MET cc_start: 0.7873 (mtm) cc_final: 0.7496 (mtp) REVERT: D 496 LEU cc_start: 0.8165 (tt) cc_final: 0.7523 (mt) REVERT: D 571 TYR cc_start: 0.8437 (m-80) cc_final: 0.8027 (m-80) REVERT: D 612 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7744 (ttm-80) outliers start: 44 outliers final: 28 residues processed: 219 average time/residue: 0.0822 time to fit residues: 27.0454 Evaluate side-chains 203 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 122 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.207612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.167096 restraints weight = 12880.460| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.24 r_work: 0.3465 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11780 Z= 0.128 Angle : 0.606 9.016 16024 Z= 0.293 Chirality : 0.043 0.287 1822 Planarity : 0.006 0.054 2040 Dihedral : 4.599 53.487 1584 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 4.23 % Allowed : 26.15 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1420 helix: 1.68 (0.22), residues: 524 sheet: -1.85 (0.37), residues: 192 loop : -1.24 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 193 TYR 0.013 0.001 TYR A 184 PHE 0.013 0.001 PHE C 136 TRP 0.037 0.001 TRP C 210 HIS 0.003 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (11780) covalent geometry : angle 0.60551 / 0.29 (16024) hydrogen bonds : bond 0.03433 / 2.18 ( 456) hydrogen bonds : angle 4.64074 / 3.28 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 630 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.8030 (mtt90) REVERT: B 64 LYS cc_start: 0.8399 (pttp) cc_final: 0.7862 (ptpp) REVERT: B 119 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 161 LYS cc_start: 0.7581 (mttm) cc_final: 0.7358 (mttm) REVERT: C 198 LEU cc_start: 0.9051 (mm) cc_final: 0.8788 (mm) REVERT: C 318 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: C 421 ASP cc_start: 0.7086 (m-30) cc_final: 0.6829 (m-30) REVERT: C 496 LEU cc_start: 0.7989 (tt) cc_final: 0.7306 (mt) REVERT: D 136 PHE cc_start: 0.7524 (p90) cc_final: 0.7292 (p90) REVERT: D 158 GLN cc_start: 0.8061 (tt0) cc_final: 0.7685 (pm20) REVERT: D 202 HIS cc_start: 0.7402 (t-90) cc_final: 0.7189 (t-90) REVERT: D 384 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: D 408 MET cc_start: 0.7684 (mtm) cc_final: 0.7436 (mtp) REVERT: D 496 LEU cc_start: 0.8115 (tt) cc_final: 0.7452 (mt) REVERT: D 571 TYR cc_start: 0.8397 (m-80) cc_final: 0.8042 (m-80) outliers start: 55 outliers final: 37 residues processed: 228 average time/residue: 0.0901 time to fit residues: 30.5988 Evaluate side-chains 211 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0030 chunk 86 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 124 ASN ** C 308 GLN ** 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 = 0.4252 r_free = 0.4252 target = 0.206848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164822 restraints weight = 12868.261| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.41 r_work: 0.3364 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11780 Z= 0.134 Angle : 0.615 10.043 16024 Z= 0.296 Chirality : 0.043 0.271 1822 Planarity : 0.006 0.054 2040 Dihedral : 4.576 52.528 1584 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.23 % Favored : 95.63 % Rotamer: Outliers : 4.69 % Allowed : 25.92 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.26 (0.23), residues: 1420 helix: 1.75 (0.22), residues: 524 sheet: -1.77 (0.37), residues: 192 loop : -1.21 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 193 TYR 0.012 0.001 TYR A 184 PHE 0.016 0.002 PHE C 215 TRP 0.035 0.001 TRP C 210 HIS 0.003 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 (11780) covalent geometry : angle 0.61530 / 0.30 (16024) hydrogen bonds : bond 0.03388 / 2.14 ( 456) hydrogen bonds : angle 4.59911 / 3.26 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 0.447 Fit side-chains REVERT: A 630 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.8011 (mtt90) REVERT: A 675 LEU cc_start: 0.8105 (mt) cc_final: 0.7863 (mt) REVERT: B 64 LYS cc_start: 0.8364 (pttp) cc_final: 0.7979 (ptpp) REVERT: B 119 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 161 LYS cc_start: 0.7552 (mttm) cc_final: 0.7307 (mttm) REVERT: C 158 GLN cc_start: 0.7232 (pm20) cc_final: 0.6943 (pm20) REVERT: C 160 GLN cc_start: 0.7764 (mp10) cc_final: 0.6941 (mp10) REVERT: C 198 LEU cc_start: 0.9088 (mm) cc_final: 0.8838 (mm) REVERT: C 318 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: C 496 LEU cc_start: 0.8103 (tt) cc_final: 0.7418 (mt) REVERT: C 612 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7615 (ttm-80) REVERT: D 158 GLN cc_start: 0.8015 (tt0) cc_final: 0.7685 (pm20) REVERT: D 255 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6975 (mtmm) REVERT: D 270 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8228 (ptmm) REVERT: D 384 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: D 408 MET cc_start: 0.7697 (mtm) cc_final: 0.7463 (mtp) REVERT: D 496 LEU cc_start: 0.8132 (tt) cc_final: 0.7448 (mt) REVERT: D 558 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8340 (tpt170) REVERT: D 571 TYR cc_start: 0.8504 (m-80) cc_final: 0.8102 (m-80) outliers start: 61 outliers final: 44 residues processed: 231 average time/residue: 0.0943 time to fit residues: 32.0280 Evaluate side-chains 223 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.205868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.160239 restraints weight = 12970.949| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.73 r_work: 0.3384 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11780 Z= 0.121 Angle : 0.607 9.155 16024 Z= 0.293 Chirality : 0.043 0.256 1822 Planarity : 0.005 0.052 2040 Dihedral : 4.508 51.533 1584 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 4.00 % Allowed : 26.85 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.17 (0.23), residues: 1420 helix: 1.78 (0.22), residues: 528 sheet: -1.72 (0.38), residues: 192 loop : -1.12 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 193 TYR 0.013 0.001 TYR A 184 PHE 0.015 0.001 PHE C 136 TRP 0.037 0.001 TRP C 210 HIS 0.003 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (11780) covalent geometry : angle 0.60663 / 0.29 (16024) hydrogen bonds : bond 0.03320 / 2.12 ( 456) hydrogen bonds : angle 4.55987 / 3.21 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.437 Fit side-chains REVERT: A 630 ARG cc_start: 0.8341 (ttp-110) cc_final: 0.8030 (mtt90) REVERT: A 675 LEU cc_start: 0.8149 (mt) cc_final: 0.7906 (mt) REVERT: B 64 LYS cc_start: 0.8351 (pttp) cc_final: 0.7983 (ptpp) REVERT: B 119 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8227 (mm) REVERT: B 157 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7831 (mt-10) REVERT: C 158 GLN cc_start: 0.7277 (pm20) cc_final: 0.6985 (pm20) REVERT: C 160 GLN cc_start: 0.7759 (mp10) cc_final: 0.6912 (mp10) REVERT: C 198 LEU cc_start: 0.9078 (mm) cc_final: 0.8835 (mm) REVERT: C 318 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: C 496 LEU cc_start: 0.8079 (tt) cc_final: 0.7408 (mt) REVERT: C 612 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6850 (mtp85) REVERT: D 158 GLN cc_start: 0.8028 (tt0) cc_final: 0.7697 (pm20) REVERT: D 215 PHE cc_start: 0.8274 (t80) cc_final: 0.8018 (t80) REVERT: D 255 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6923 (mtmm) REVERT: D 270 LYS cc_start: 0.8550 (ptmm) cc_final: 0.8241 (ptmm) REVERT: D 384 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: D 496 LEU cc_start: 0.8115 (tt) cc_final: 0.7436 (mt) REVERT: D 558 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8357 (tpt170) REVERT: D 571 TYR cc_start: 0.8468 (m-80) cc_final: 0.8100 (m-80) outliers start: 52 outliers final: 38 residues processed: 217 average time/residue: 0.0955 time to fit residues: 30.7971 Evaluate side-chains 217 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 0.0060 chunk 11 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN D 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.207458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163738 restraints weight = 12662.692| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.58 r_work: 0.3412 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11780 Z= 0.131 Angle : 0.611 9.111 16024 Z= 0.294 Chirality : 0.043 0.228 1822 Planarity : 0.005 0.053 2040 Dihedral : 4.470 49.711 1584 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 3.85 % Allowed : 27.23 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.08 (0.23), residues: 1420 helix: 1.84 (0.22), residues: 528 sheet: -1.67 (0.38), residues: 192 loop : -1.07 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 96 TYR 0.012 0.001 TYR A 184 PHE 0.016 0.002 PHE C 136 TRP 0.039 0.001 TRP C 210 HIS 0.004 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (11780) covalent geometry : angle 0.61072 / 0.29 (16024) hydrogen bonds : bond 0.03328 / 2.11 ( 456) hydrogen bonds : angle 4.51874 / 3.20 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.462 Fit side-chains REVERT: A 630 ARG cc_start: 0.8457 (ttp-110) cc_final: 0.8068 (mtt90) REVERT: A 675 LEU cc_start: 0.8234 (mt) cc_final: 0.7951 (mt) REVERT: B 64 LYS cc_start: 0.8424 (pttp) cc_final: 0.8090 (ptpp) REVERT: B 96 ARG cc_start: 0.8062 (ptp-110) cc_final: 0.7729 (ttm110) REVERT: B 655 MET cc_start: 0.8113 (mmm) cc_final: 0.7827 (tpt) REVERT: C 158 GLN cc_start: 0.7114 (pm20) cc_final: 0.6865 (pm20) REVERT: C 160 GLN cc_start: 0.7790 (mp10) cc_final: 0.6912 (mp10) REVERT: C 198 LEU cc_start: 0.9051 (mm) cc_final: 0.8825 (mm) REVERT: C 612 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6875 (mtp85) REVERT: D 113 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (pp) REVERT: D 158 GLN cc_start: 0.8025 (tt0) cc_final: 0.7741 (pm20) REVERT: D 255 LYS cc_start: 0.7215 (mtmm) cc_final: 0.6974 (mtmm) REVERT: D 270 LYS cc_start: 0.8549 (ptmm) cc_final: 0.8315 (ptmm) REVERT: D 384 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: D 496 LEU cc_start: 0.8131 (tt) cc_final: 0.7423 (mt) REVERT: D 558 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8338 (tpt90) REVERT: D 571 TYR cc_start: 0.8513 (m-80) cc_final: 0.8119 (m-80) outliers start: 50 outliers final: 38 residues processed: 213 average time/residue: 0.1033 time to fit residues: 32.3937 Evaluate side-chains 210 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 10 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 125 optimal weight: 0.1980 chunk 36 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 120 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.208597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.164190 restraints weight = 12620.421| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.58 r_work: 0.3407 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11780 Z= 0.120 Angle : 0.621 11.011 16024 Z= 0.297 Chirality : 0.043 0.243 1822 Planarity : 0.006 0.062 2040 Dihedral : 4.076 28.931 1580 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 3.31 % Allowed : 27.85 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.00 (0.23), residues: 1420 helix: 1.90 (0.22), residues: 528 sheet: -1.66 (0.38), residues: 192 loop : -1.00 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 96 TYR 0.013 0.001 TYR A 184 PHE 0.015 0.001 PHE C 136 TRP 0.030 0.001 TRP C 210 HIS 0.003 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (11780) covalent geometry : angle 0.62069 / 0.30 (16024) hydrogen bonds : bond 0.03181 / 2.02 ( 456) hydrogen bonds : angle 4.51700 / 3.18 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.5963 (tp30) REVERT: A 630 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8064 (mtt90) REVERT: A 675 LEU cc_start: 0.8217 (mt) cc_final: 0.7949 (mt) REVERT: B 64 LYS cc_start: 0.8419 (pttp) cc_final: 0.8064 (ptpp) REVERT: B 96 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7710 (ttm110) REVERT: B 157 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 198 LEU cc_start: 0.9052 (mm) cc_final: 0.8838 (mm) REVERT: C 612 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6813 (mtp85) REVERT: D 158 GLN cc_start: 0.8059 (tt0) cc_final: 0.7726 (pm20) REVERT: D 255 LYS cc_start: 0.7152 (mtmm) cc_final: 0.6910 (mtmm) REVERT: D 270 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8285 (ptmm) REVERT: D 384 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: D 496 LEU cc_start: 0.8142 (tt) cc_final: 0.7452 (mt) REVERT: D 558 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8366 (tpt90) REVERT: D 571 TYR cc_start: 0.8464 (m-80) cc_final: 0.8086 (m-80) outliers start: 43 outliers final: 37 residues processed: 216 average time/residue: 0.0940 time to fit residues: 30.3310 Evaluate side-chains 215 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 94 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 123 optimal weight: 0.0570 chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN D 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.207701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163235 restraints weight = 12755.785| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.55 r_work: 0.3390 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11780 Z= 0.121 Angle : 0.631 10.623 16024 Z= 0.300 Chirality : 0.043 0.263 1822 Planarity : 0.006 0.052 2040 Dihedral : 4.076 28.980 1580 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 3.31 % Allowed : 28.15 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.06 (0.23), residues: 1420 helix: 1.93 (0.22), residues: 528 sheet: -1.70 (0.39), residues: 182 loop : -0.94 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 193 TYR 0.012 0.001 TYR A 184 PHE 0.040 0.002 PHE C 134 TRP 0.027 0.001 TRP C 210 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (11780) covalent geometry : angle 0.63070 / 0.30 (16024) hydrogen bonds : bond 0.03206 / 2.05 ( 456) hydrogen bonds : angle 4.49803 / 3.17 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.404 Fit side-chains REVERT: A 630 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8042 (mtt90) REVERT: A 675 LEU cc_start: 0.8210 (mt) cc_final: 0.7953 (mt) REVERT: B 64 LYS cc_start: 0.8392 (pttp) cc_final: 0.8020 (ptpp) REVERT: B 96 ARG cc_start: 0.8037 (ptp-110) cc_final: 0.7734 (ttm110) REVERT: B 153 ASP cc_start: 0.7757 (t0) cc_final: 0.7382 (t70) REVERT: B 157 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 160 GLN cc_start: 0.7675 (mp10) cc_final: 0.6851 (mp10) REVERT: C 198 LEU cc_start: 0.9029 (mm) cc_final: 0.8816 (mm) REVERT: C 612 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7596 (ttm-80) REVERT: D 158 GLN cc_start: 0.8112 (tt0) cc_final: 0.7751 (pm20) REVERT: D 255 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6946 (mtmm) REVERT: D 270 LYS cc_start: 0.8515 (ptmm) cc_final: 0.8281 (ptmm) REVERT: D 384 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: D 496 LEU cc_start: 0.8124 (tt) cc_final: 0.7421 (mt) REVERT: D 558 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8380 (tpt90) REVERT: D 571 TYR cc_start: 0.8460 (m-80) cc_final: 0.8084 (m-80) outliers start: 43 outliers final: 38 residues processed: 205 average time/residue: 0.0952 time to fit residues: 28.7161 Evaluate side-chains 210 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 652 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 382 ASN D 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.206000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162345 restraints weight = 13008.603| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.53 r_work: 0.3422 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11780 Z= 0.147 Angle : 0.659 11.759 16024 Z= 0.312 Chirality : 0.044 0.254 1822 Planarity : 0.006 0.052 2040 Dihedral : 4.117 28.074 1580 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 3.62 % Allowed : 27.85 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.02 (0.23), residues: 1420 helix: 1.85 (0.22), residues: 528 sheet: -1.66 (0.39), residues: 190 loop : -0.93 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 193 TYR 0.011 0.001 TYR B 184 PHE 0.016 0.002 PHE C 136 TRP 0.019 0.001 TRP C 210 HIS 0.004 0.001 HIS D 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (11780) covalent geometry : angle 0.65891 / 0.31 (16024) hydrogen bonds : bond 0.03377 / 2.15 ( 456) hydrogen bonds : angle 4.54765 / 3.20 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.27 seconds wall clock time: 43 minutes 8.80 seconds (2588.80 seconds total)