Starting phenix.real_space_refine on Thu Jul 24 15:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.map" model { file = "/net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xvg_33486/07_2025/7xvg_33486.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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 26 5.16 5 C 4160 2.51 5 N 1066 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6438 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3327 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3111 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 368} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.46, per 1000 atoms: 0.69 Number of scatterers: 6438 At special positions: 0 Unit cell: (75.6, 94.08, 110.04, 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 26 16.00 O 1186 8.00 N 1066 7.00 C 4160 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: 1.51 Conformation dependent library (CDL) restraints added in 928.1 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1510 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 50.5% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 469 through 482 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.835A pdb=" N ASP A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.532A pdb=" N LEU A 598 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.701A pdb=" N ILE A 618 " --> pdb=" O PRO A 615 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 619 " --> pdb=" O MET A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.672A pdb=" N VAL A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 707 through 718 removed outlier: 4.170A pdb=" N LEU A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.833A pdb=" N PHE A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.719A pdb=" N PHE A 844 " --> pdb=" O PRO A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.795A pdb=" N ILE A 864 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 removed outlier: 4.252A pdb=" N TYR B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.560A pdb=" N ASN B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.365A pdb=" N ILE B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 199' Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.984A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.552A pdb=" N ILE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 275 " --> pdb=" O HIS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.530A pdb=" N LYS B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.680A pdb=" N ILE B 322 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 removed outlier: 4.281A pdb=" N ASP B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 329 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.565A pdb=" N SER B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 335' Processing helix chain 'B' and resid 336 through 347 removed outlier: 4.094A pdb=" N LEU B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.835A pdb=" N SER B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 393 through 396 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 423 through 441 removed outlier: 3.597A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.757A pdb=" N LEU B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 483 Processing helix chain 'B' and resid 508 through 529 removed outlier: 4.253A pdb=" N LYS B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 553 removed outlier: 3.556A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.538A pdb=" N VAL A 496 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 490 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 500 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 486 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628 removed outlier: 6.848A pdb=" N LEU A 627 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 672 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG A 697 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 699 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 725 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802 removed outlier: 7.512A pdb=" N LEU A 800 " --> pdb=" O ARG A 833 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 859 removed outlier: 3.857A pdb=" N PHE A 857 " --> pdb=" O ARG A 881 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 645 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: 1.84 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1132 1.32 - 1.44: 1657 1.44 - 1.57: 3744 1.57 - 1.69: 1 1.69 - 1.81: 42 Bond restraints: 6576 Sorted by residual: bond pdb=" N LEU A 879 " pdb=" CA LEU A 879 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.36e-02 5.41e+03 6.95e+00 bond pdb=" C PRO A 877 " pdb=" O PRO A 877 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" N SER A 878 " pdb=" CA SER A 878 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" CA SER A 878 " pdb=" CB SER A 878 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.11e+00 bond pdb=" N LEU A 690 " pdb=" CA LEU A 690 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.23e-02 6.61e+03 5.05e+00 ... (remaining 6571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 8666 2.05 - 4.10: 179 4.10 - 6.15: 28 6.15 - 8.19: 6 8.19 - 10.24: 3 Bond angle restraints: 8882 Sorted by residual: angle pdb=" N ILE B 318 " pdb=" CA ILE B 318 " pdb=" C ILE B 318 " ideal model delta sigma weight residual 111.91 108.20 3.71 8.90e-01 1.26e+00 1.73e+01 angle pdb=" N GLU A 478 " pdb=" CA GLU A 478 " pdb=" CB GLU A 478 " ideal model delta sigma weight residual 110.28 116.49 -6.21 1.55e+00 4.16e-01 1.61e+01 angle pdb=" N ARG A 689 " pdb=" CA ARG A 689 " pdb=" C ARG A 689 " ideal model delta sigma weight residual 112.89 108.19 4.70 1.24e+00 6.50e-01 1.43e+01 angle pdb=" C ASN A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta sigma weight residual 120.31 115.12 5.19 1.52e+00 4.33e-01 1.17e+01 angle pdb=" C PRO A 850 " pdb=" N ARG A 851 " pdb=" CA ARG A 851 " ideal model delta sigma weight residual 122.56 117.89 4.67 1.50e+00 4.44e-01 9.71e+00 ... (remaining 8877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3547 17.95 - 35.90: 360 35.90 - 53.86: 45 53.86 - 71.81: 10 71.81 - 89.76: 5 Dihedral angle restraints: 3967 sinusoidal: 1638 harmonic: 2329 Sorted by residual: dihedral pdb=" CA LEU A 693 " pdb=" C LEU A 693 " pdb=" N ARG A 694 " pdb=" CA ARG A 694 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CG ARG A 689 " pdb=" CD ARG A 689 " pdb=" NE ARG A 689 " pdb=" CZ ARG A 689 " ideal model delta sinusoidal sigma weight residual -90.00 -32.90 -57.10 2 1.50e+01 4.44e-03 1.50e+01 dihedral pdb=" CA LEU B 267 " pdb=" C LEU B 267 " pdb=" N GLN B 268 " pdb=" CA GLN B 268 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 761 0.052 - 0.103: 195 0.103 - 0.155: 37 0.155 - 0.207: 0 0.207 - 0.259: 3 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA ARG A 689 " pdb=" N ARG A 689 " pdb=" C ARG A 689 " pdb=" CB ARG A 689 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 869 " pdb=" CA ILE A 869 " pdb=" CG1 ILE A 869 " pdb=" CG2 ILE A 869 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LEU A 879 " pdb=" N LEU A 879 " pdb=" C LEU A 879 " pdb=" CB LEU A 879 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 993 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 688 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C GLY A 688 " 0.069 2.00e-02 2.50e+03 pdb=" O GLY A 688 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 689 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 876 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.24e+01 pdb=" C LEU A 876 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU A 876 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 877 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 689 " -0.161 9.50e-02 1.11e+02 7.23e-02 3.21e+00 pdb=" NE ARG A 689 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 689 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 689 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 689 " -0.006 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 84 2.64 - 3.20: 6170 3.20 - 3.77: 9567 3.77 - 4.33: 12956 4.33 - 4.90: 20683 Nonbonded interactions: 49460 Sorted by model distance: nonbonded pdb=" CD2 LEU A 879 " pdb=" N GLN A 880 " model vdw 2.074 3.540 nonbonded pdb=" O THR A 691 " pdb=" OG1 THR A 691 " model vdw 2.155 3.040 nonbonded pdb=" O GLU B 222 " pdb=" OG1 THR B 226 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 842 " pdb=" O ASN A 868 " model vdw 2.214 3.040 nonbonded pdb=" O GLU A 713 " pdb=" OG SER A 716 " model vdw 2.265 3.040 ... (remaining 49455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6576 Z= 0.178 Angle : 0.728 10.242 8882 Z= 0.381 Chirality : 0.048 0.259 996 Planarity : 0.005 0.072 1116 Dihedral : 14.260 89.760 2457 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 0.28 % Allowed : 0.83 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 780 helix: 0.51 (0.30), residues: 325 sheet: -2.62 (0.73), residues: 59 loop : -1.30 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.005 0.001 HIS B 359 PHE 0.028 0.002 PHE B 233 TYR 0.015 0.001 TYR A 460 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.19403 ( 230) hydrogen bonds : angle 6.18500 ( 645) covalent geometry : bond 0.00370 ( 6576) covalent geometry : angle 0.72776 ( 8882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8144 (pm20) cc_final: 0.7928 (pm20) REVERT: B 195 ASP cc_start: 0.8268 (m-30) cc_final: 0.7995 (t0) REVERT: B 501 PHE cc_start: 0.7888 (m-80) cc_final: 0.7556 (m-80) REVERT: B 516 VAL cc_start: 0.8205 (t) cc_final: 0.7780 (t) outliers start: 2 outliers final: 2 residues processed: 107 average time/residue: 0.1759 time to fit residues: 25.9966 Evaluate side-chains 87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 691 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 729 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.122183 restraints weight = 11218.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123512 restraints weight = 6223.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.124454 restraints weight = 5268.444| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6576 Z= 0.123 Angle : 0.655 10.154 8882 Z= 0.318 Chirality : 0.044 0.138 996 Planarity : 0.004 0.040 1116 Dihedral : 4.887 56.816 859 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.97 % Allowed : 10.62 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.30), residues: 780 helix: 0.51 (0.29), residues: 335 sheet: -2.73 (0.69), residues: 61 loop : -1.38 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 453 HIS 0.008 0.001 HIS A 502 PHE 0.021 0.001 PHE A 703 TYR 0.014 0.001 TYR B 383 ARG 0.004 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 230) hydrogen bonds : angle 4.65173 ( 645) covalent geometry : bond 0.00269 ( 6576) covalent geometry : angle 0.65532 ( 8882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 ILE cc_start: 0.6964 (tp) cc_final: 0.6717 (tp) REVERT: A 669 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 682 ASP cc_start: 0.8273 (p0) cc_final: 0.7714 (p0) REVERT: A 809 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 195 ASP cc_start: 0.8429 (m-30) cc_final: 0.8158 (t0) REVERT: B 233 PHE cc_start: 0.7435 (t80) cc_final: 0.7162 (t80) REVERT: B 501 PHE cc_start: 0.7996 (m-80) cc_final: 0.7584 (m-10) outliers start: 7 outliers final: 3 residues processed: 98 average time/residue: 0.1958 time to fit residues: 26.5755 Evaluate side-chains 89 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115611 restraints weight = 11251.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117704 restraints weight = 6975.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118290 restraints weight = 6067.423| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6576 Z= 0.190 Angle : 0.681 9.201 8882 Z= 0.339 Chirality : 0.046 0.147 996 Planarity : 0.004 0.041 1116 Dihedral : 4.645 17.870 854 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.21 % Allowed : 13.93 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.31), residues: 780 helix: 0.31 (0.29), residues: 334 sheet: -3.09 (0.64), residues: 65 loop : -1.30 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.007 0.001 HIS B 359 PHE 0.023 0.002 PHE A 703 TYR 0.021 0.002 TYR A 799 ARG 0.004 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 230) hydrogen bonds : angle 4.72010 ( 645) covalent geometry : bond 0.00445 ( 6576) covalent geometry : angle 0.68096 ( 8882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7856 (tt0) cc_final: 0.7108 (pm20) REVERT: A 585 GLU cc_start: 0.7900 (pp20) cc_final: 0.7615 (pm20) REVERT: A 682 ASP cc_start: 0.8345 (p0) cc_final: 0.7996 (p0) REVERT: A 881 ARG cc_start: 0.6531 (tpm170) cc_final: 0.6324 (tpm170) REVERT: B 501 PHE cc_start: 0.7987 (m-80) cc_final: 0.7514 (m-10) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.2271 time to fit residues: 31.2645 Evaluate side-chains 94 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119711 restraints weight = 11368.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122424 restraints weight = 6231.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123065 restraints weight = 5479.646| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6576 Z= 0.118 Angle : 0.621 9.015 8882 Z= 0.304 Chirality : 0.043 0.139 996 Planarity : 0.004 0.041 1116 Dihedral : 4.371 18.802 854 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.17 % Allowed : 16.28 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.31), residues: 780 helix: 0.52 (0.29), residues: 333 sheet: -2.72 (0.66), residues: 61 loop : -1.22 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 356 HIS 0.004 0.001 HIS B 359 PHE 0.021 0.001 PHE A 703 TYR 0.014 0.001 TYR B 383 ARG 0.003 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 230) hydrogen bonds : angle 4.41756 ( 645) covalent geometry : bond 0.00265 ( 6576) covalent geometry : angle 0.62106 ( 8882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7881 (pp20) cc_final: 0.7215 (pm20) REVERT: A 718 MET cc_start: 0.7337 (pmm) cc_final: 0.6985 (pmm) REVERT: A 873 MET cc_start: 0.3531 (OUTLIER) cc_final: 0.3261 (mmm) REVERT: A 881 ARG cc_start: 0.6304 (tpm170) cc_final: 0.5959 (tpm170) REVERT: B 437 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 501 PHE cc_start: 0.7973 (m-80) cc_final: 0.7540 (m-10) outliers start: 23 outliers final: 15 residues processed: 112 average time/residue: 0.1554 time to fit residues: 24.5901 Evaluate side-chains 103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118246 restraints weight = 11153.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120061 restraints weight = 6409.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120895 restraints weight = 5193.039| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6576 Z= 0.137 Angle : 0.629 12.050 8882 Z= 0.308 Chirality : 0.044 0.147 996 Planarity : 0.004 0.039 1116 Dihedral : 4.336 20.808 854 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.72 % Allowed : 17.93 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 780 helix: 0.56 (0.29), residues: 334 sheet: -2.71 (0.67), residues: 61 loop : -1.19 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 356 HIS 0.005 0.001 HIS B 359 PHE 0.019 0.002 PHE A 703 TYR 0.013 0.001 TYR B 383 ARG 0.003 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 230) hydrogen bonds : angle 4.39257 ( 645) covalent geometry : bond 0.00319 ( 6576) covalent geometry : angle 0.62917 ( 8882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8234 (pm20) cc_final: 0.7967 (pm20) REVERT: A 585 GLU cc_start: 0.7925 (pp20) cc_final: 0.7345 (pm20) REVERT: A 721 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6970 (mt) REVERT: A 873 MET cc_start: 0.4037 (OUTLIER) cc_final: 0.3787 (mmm) REVERT: A 881 ARG cc_start: 0.6333 (tpm170) cc_final: 0.5389 (tpt90) REVERT: B 501 PHE cc_start: 0.7899 (m-80) cc_final: 0.7502 (m-10) outliers start: 27 outliers final: 15 residues processed: 107 average time/residue: 0.1677 time to fit residues: 25.6280 Evaluate side-chains 99 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116422 restraints weight = 11237.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120618 restraints weight = 5923.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123263 restraints weight = 4121.089| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6576 Z= 0.109 Angle : 0.625 11.754 8882 Z= 0.301 Chirality : 0.042 0.139 996 Planarity : 0.003 0.035 1116 Dihedral : 4.160 21.178 854 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.31 % Allowed : 18.76 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.31), residues: 780 helix: 0.74 (0.29), residues: 335 sheet: -2.70 (0.62), residues: 66 loop : -1.14 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.012 0.001 HIS B 509 PHE 0.017 0.001 PHE A 703 TYR 0.013 0.001 TYR B 383 ARG 0.003 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 230) hydrogen bonds : angle 4.28075 ( 645) covalent geometry : bond 0.00239 ( 6576) covalent geometry : angle 0.62484 ( 8882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7903 (pp20) cc_final: 0.7255 (pm20) REVERT: A 662 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 718 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6818 (pmm) REVERT: A 721 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6919 (mt) REVERT: A 881 ARG cc_start: 0.6223 (tpm170) cc_final: 0.5274 (tpt90) REVERT: B 232 GLU cc_start: 0.8275 (tp30) cc_final: 0.7935 (tp30) REVERT: B 501 PHE cc_start: 0.7941 (m-80) cc_final: 0.7544 (m-10) outliers start: 24 outliers final: 17 residues processed: 105 average time/residue: 0.1653 time to fit residues: 24.2232 Evaluate side-chains 107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.153078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118612 restraints weight = 11328.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120811 restraints weight = 6408.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121665 restraints weight = 5028.870| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6576 Z= 0.132 Angle : 0.633 11.336 8882 Z= 0.308 Chirality : 0.043 0.133 996 Planarity : 0.004 0.047 1116 Dihedral : 4.162 19.171 854 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.72 % Allowed : 18.48 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 780 helix: 0.76 (0.29), residues: 333 sheet: -2.78 (0.62), residues: 67 loop : -1.11 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.007 0.001 HIS B 509 PHE 0.019 0.001 PHE B 233 TYR 0.013 0.001 TYR B 383 ARG 0.008 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 230) hydrogen bonds : angle 4.26303 ( 645) covalent geometry : bond 0.00306 ( 6576) covalent geometry : angle 0.63292 ( 8882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8159 (pm20) cc_final: 0.7901 (pm20) REVERT: A 508 LEU cc_start: 0.8089 (tt) cc_final: 0.7545 (mt) REVERT: A 585 GLU cc_start: 0.7903 (pp20) cc_final: 0.7332 (pm20) REVERT: A 713 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: A 721 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7084 (mt) REVERT: B 232 GLU cc_start: 0.8211 (tp30) cc_final: 0.7966 (tp30) REVERT: B 238 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: B 318 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8318 (pt) REVERT: B 472 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 501 PHE cc_start: 0.7954 (m-80) cc_final: 0.7550 (m-10) outliers start: 27 outliers final: 17 residues processed: 103 average time/residue: 0.1687 time to fit residues: 24.1301 Evaluate side-chains 107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119134 restraints weight = 11282.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120483 restraints weight = 7152.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122150 restraints weight = 5092.384| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6576 Z= 0.112 Angle : 0.630 11.398 8882 Z= 0.305 Chirality : 0.042 0.131 996 Planarity : 0.004 0.084 1116 Dihedral : 4.157 20.664 854 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.31 % Allowed : 19.03 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 780 helix: 0.81 (0.30), residues: 332 sheet: -2.69 (0.62), residues: 66 loop : -1.08 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.005 0.001 HIS B 359 PHE 0.018 0.001 PHE A 703 TYR 0.014 0.001 TYR A 460 ARG 0.009 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 230) hydrogen bonds : angle 4.17742 ( 645) covalent geometry : bond 0.00254 ( 6576) covalent geometry : angle 0.62970 ( 8882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8006 (tt) cc_final: 0.7494 (mt) REVERT: A 585 GLU cc_start: 0.7875 (pp20) cc_final: 0.7287 (pm20) REVERT: A 628 ASP cc_start: 0.8288 (t0) cc_final: 0.7910 (t0) REVERT: A 713 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: B 232 GLU cc_start: 0.8262 (tp30) cc_final: 0.8059 (tp30) REVERT: B 238 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: B 318 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (pt) REVERT: B 472 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 501 PHE cc_start: 0.7986 (m-80) cc_final: 0.7572 (m-10) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.1660 time to fit residues: 25.3987 Evaluate side-chains 108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.153561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119206 restraints weight = 11325.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120252 restraints weight = 6415.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121455 restraints weight = 5955.955| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6576 Z= 0.122 Angle : 0.641 11.367 8882 Z= 0.309 Chirality : 0.043 0.134 996 Planarity : 0.004 0.079 1116 Dihedral : 4.150 17.642 854 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 19.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.31), residues: 780 helix: 0.80 (0.29), residues: 332 sheet: -2.68 (0.62), residues: 66 loop : -1.07 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.007 0.001 HIS B 509 PHE 0.018 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.010 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 230) hydrogen bonds : angle 4.16934 ( 645) covalent geometry : bond 0.00283 ( 6576) covalent geometry : angle 0.64138 ( 8882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8035 (tt) cc_final: 0.7491 (mt) REVERT: A 585 GLU cc_start: 0.7868 (pp20) cc_final: 0.7319 (pm20) REVERT: A 713 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: B 238 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8332 (mp10) REVERT: B 318 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8320 (pt) REVERT: B 472 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 501 PHE cc_start: 0.7963 (m-80) cc_final: 0.7561 (m-10) outliers start: 23 outliers final: 16 residues processed: 106 average time/residue: 0.1655 time to fit residues: 24.5792 Evaluate side-chains 107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.152800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118640 restraints weight = 11538.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119655 restraints weight = 6530.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120700 restraints weight = 5368.305| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6576 Z= 0.129 Angle : 0.659 11.474 8882 Z= 0.319 Chirality : 0.043 0.163 996 Planarity : 0.004 0.076 1116 Dihedral : 4.177 17.375 854 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.31 % Allowed : 19.45 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.31), residues: 780 helix: 0.79 (0.29), residues: 331 sheet: -2.54 (0.67), residues: 59 loop : -1.12 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.005 0.001 HIS B 359 PHE 0.017 0.001 PHE A 703 TYR 0.015 0.001 TYR A 460 ARG 0.011 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 230) hydrogen bonds : angle 4.19097 ( 645) covalent geometry : bond 0.00302 ( 6576) covalent geometry : angle 0.65881 ( 8882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8009 (tt) cc_final: 0.7475 (mt) REVERT: A 585 GLU cc_start: 0.7900 (pp20) cc_final: 0.7357 (pm20) REVERT: A 713 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: A 881 ARG cc_start: 0.5992 (tpm170) cc_final: 0.5718 (tpm170) REVERT: B 238 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: B 472 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 501 PHE cc_start: 0.7997 (m-80) cc_final: 0.7590 (m-10) outliers start: 24 outliers final: 19 residues processed: 106 average time/residue: 0.1596 time to fit residues: 23.7848 Evaluate side-chains 109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.0010 chunk 6 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.151576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119967 restraints weight = 11208.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118687 restraints weight = 7328.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120499 restraints weight = 6375.270| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6576 Z= 0.165 Angle : 0.668 11.250 8882 Z= 0.328 Chirality : 0.045 0.138 996 Planarity : 0.004 0.073 1116 Dihedral : 4.287 17.549 854 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.45 % Allowed : 19.86 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.31), residues: 780 helix: 0.70 (0.29), residues: 332 sheet: -3.09 (0.61), residues: 67 loop : -1.14 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.006 0.001 HIS B 359 PHE 0.018 0.002 PHE B 448 TYR 0.016 0.001 TYR A 799 ARG 0.011 0.001 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 230) hydrogen bonds : angle 4.29607 ( 645) covalent geometry : bond 0.00389 ( 6576) covalent geometry : angle 0.66842 ( 8882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.59 seconds wall clock time: 41 minutes 24.66 seconds (2484.66 seconds total)