Starting phenix.real_space_refine on Fri Dec 27 18:32:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xvg_33486/12_2024/7xvg_33486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xvg_33486/12_2024/7xvg_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_33486/12_2024/7xvg_33486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xvg_33486/12_2024/7xvg_33486.map" model { file = "/net/cci-nas-00/data/ceres_data/7xvg_33486/12_2024/7xvg_33486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xvg_33486/12_2024/7xvg_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-5532/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: 1.39 Conformation dependent library (CDL) restraints added in 947.0 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: 0.71 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: 1.52 Time building geometry restraints manager: 1.63 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: 1.140 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.650 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- 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= 0.243 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 *********************** 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 : 0.757 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: 0.1711 time to fit residues: 24.9660 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 : 0.669 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.5598 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1223 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= 0.179 Angle : 0.654 10.200 8882 Z= 0.317 Chirality : 0.044 0.138 996 Planarity : 0.004 0.041 1116 Dihedral : 4.884 57.474 859 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.83 % Allowed : 10.76 % 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: -1.01 (0.30), residues: 780 helix: 0.52 (0.29), residues: 333 sheet: -2.74 (0.69), residues: 61 loop : -1.38 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 453 HIS 0.007 0.001 HIS A 502 PHE 0.021 0.001 PHE A 703 TYR 0.014 0.001 TYR B 383 ARG 0.003 0.000 ARG A 448 *********************** 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 105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8320 (pm20) cc_final: 0.8114 (pm20) REVERT: A 502 HIS cc_start: 0.7299 (t70) cc_final: 0.7094 (t-90) REVERT: A 634 ILE cc_start: 0.6861 (tp) cc_final: 0.6622 (tp) REVERT: A 669 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 682 ASP cc_start: 0.8200 (p0) cc_final: 0.7676 (p0) REVERT: A 809 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 233 PHE cc_start: 0.7247 (t80) cc_final: 0.7006 (t80) REVERT: B 501 PHE cc_start: 0.7852 (m-80) cc_final: 0.7521 (m-10) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.1700 time to fit residues: 23.4808 Evaluate side-chains 90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 39 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6576 Z= 0.163 Angle : 0.601 9.545 8882 Z= 0.292 Chirality : 0.043 0.139 996 Planarity : 0.004 0.038 1116 Dihedral : 4.233 17.781 854 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.07 % Allowed : 12.83 % Favored : 85.10 % 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: -0.92 (0.31), residues: 780 helix: 0.53 (0.29), residues: 333 sheet: -2.59 (0.68), residues: 61 loop : -1.28 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 453 HIS 0.004 0.001 HIS B 359 PHE 0.021 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG A 689 *********************** 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 106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8800 (mmp80) cc_final: 0.8367 (mmp80) REVERT: A 486 GLN cc_start: 0.8336 (pm20) cc_final: 0.8086 (pm20) REVERT: A 502 HIS cc_start: 0.7289 (t70) cc_final: 0.7067 (t70) REVERT: A 585 GLU cc_start: 0.7707 (pp20) cc_final: 0.7341 (pm20) REVERT: A 634 ILE cc_start: 0.6835 (tp) cc_final: 0.6547 (tp) REVERT: A 682 ASP cc_start: 0.8147 (p0) cc_final: 0.7815 (p0) REVERT: B 501 PHE cc_start: 0.7868 (m-80) cc_final: 0.7533 (m-10) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.1597 time to fit residues: 22.1660 Evaluate side-chains 91 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 465 LEU Chi-restraints excluded: chain B residue 509 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1723 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= 0.198 Angle : 0.607 8.817 8882 Z= 0.300 Chirality : 0.043 0.135 996 Planarity : 0.004 0.038 1116 Dihedral : 4.205 18.544 854 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.76 % Allowed : 15.31 % Favored : 81.93 % 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: -0.86 (0.31), residues: 780 helix: 0.57 (0.29), residues: 333 sheet: -2.75 (0.66), residues: 63 loop : -1.18 (0.32), residues: 384 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 0.020 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG A 689 *********************** 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 114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8376 (pm20) cc_final: 0.7949 (pm20) REVERT: A 502 HIS cc_start: 0.7149 (t70) cc_final: 0.6919 (t-90) REVERT: A 585 GLU cc_start: 0.7766 (pp20) cc_final: 0.7065 (pm20) REVERT: A 634 ILE cc_start: 0.6903 (tp) cc_final: 0.6690 (tp) REVERT: A 718 MET cc_start: 0.7465 (pmm) cc_final: 0.7160 (pmm) REVERT: B 437 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8398 (tt) REVERT: B 501 PHE cc_start: 0.7882 (m-80) cc_final: 0.7527 (m-10) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 0.1624 time to fit residues: 24.1397 Evaluate side-chains 95 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET 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 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL 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 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6576 Z= 0.174 Angle : 0.621 11.771 8882 Z= 0.300 Chirality : 0.043 0.152 996 Planarity : 0.004 0.038 1116 Dihedral : 4.132 20.789 854 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.34 % Allowed : 17.38 % Favored : 80.28 % 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: -0.73 (0.31), residues: 780 helix: 0.71 (0.29), residues: 333 sheet: -2.66 (0.62), residues: 67 loop : -1.12 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 356 HIS 0.004 0.001 HIS B 359 PHE 0.018 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.002 0.000 ARG A 448 *********************** 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 109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 HIS cc_start: 0.7076 (t70) cc_final: 0.6828 (t-90) REVERT: A 585 GLU cc_start: 0.7758 (pp20) cc_final: 0.7094 (pm20) REVERT: A 634 ILE cc_start: 0.6895 (tp) cc_final: 0.6581 (tp) REVERT: A 881 ARG cc_start: 0.6127 (tpm170) cc_final: 0.4125 (mtp180) REVERT: B 501 PHE cc_start: 0.7835 (m-80) cc_final: 0.7512 (m-10) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1615 time to fit residues: 22.5759 Evaluate side-chains 95 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET 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 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 240 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 72 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6576 Z= 0.252 Angle : 0.655 11.268 8882 Z= 0.321 Chirality : 0.045 0.141 996 Planarity : 0.004 0.039 1116 Dihedral : 4.240 21.196 854 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.90 % Allowed : 17.79 % Favored : 79.31 % 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: 0.67 (0.29), residues: 334 sheet: -2.84 (0.62), residues: 69 loop : -1.15 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 856 HIS 0.009 0.001 HIS B 509 PHE 0.018 0.002 PHE A 703 TYR 0.016 0.001 TYR A 799 ARG 0.003 0.000 ARG A 689 *********************** 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 109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7933 (pp20) cc_final: 0.7326 (pm20) REVERT: A 634 ILE cc_start: 0.7046 (tp) cc_final: 0.6834 (tp) REVERT: A 721 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6970 (mt) REVERT: B 232 GLU cc_start: 0.8178 (tp30) cc_final: 0.7877 (tp30) REVERT: B 437 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8442 (tt) REVERT: B 501 PHE cc_start: 0.7881 (m-80) cc_final: 0.7513 (m-10) outliers start: 21 outliers final: 16 residues processed: 99 average time/residue: 0.1602 time to fit residues: 22.2240 Evaluate side-chains 102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 484 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6576 Z= 0.300 Angle : 0.695 10.912 8882 Z= 0.342 Chirality : 0.046 0.145 996 Planarity : 0.004 0.044 1116 Dihedral : 4.438 19.239 854 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.00 % Allowed : 17.52 % Favored : 78.48 % 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: -0.94 (0.31), residues: 780 helix: 0.57 (0.29), residues: 334 sheet: -3.23 (0.59), residues: 73 loop : -1.11 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.019 0.002 HIS B 509 PHE 0.018 0.002 PHE B 233 TYR 0.019 0.002 TYR A 799 ARG 0.007 0.001 ARG B 186 *********************** 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 123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7817 (tt0) cc_final: 0.7178 (pm20) REVERT: A 585 GLU cc_start: 0.7984 (pp20) cc_final: 0.7410 (pm20) REVERT: A 713 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: A 721 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 318 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8353 (pt) REVERT: B 437 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8406 (tt) REVERT: B 472 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 501 PHE cc_start: 0.7916 (m-80) cc_final: 0.7509 (m-10) outliers start: 29 outliers final: 17 residues processed: 111 average time/residue: 0.1621 time to fit residues: 24.9410 Evaluate side-chains 106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 713 GLU 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 779 THR Chi-restraints excluded: chain A residue 780 LEU 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 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 437 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 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6576 Z= 0.191 Angle : 0.663 11.091 8882 Z= 0.319 Chirality : 0.043 0.135 996 Planarity : 0.004 0.083 1116 Dihedral : 4.343 21.367 854 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.62 % Allowed : 19.45 % 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: -0.69 (0.31), residues: 780 helix: 0.70 (0.29), residues: 333 sheet: -2.80 (0.62), residues: 67 loop : -1.01 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 356 HIS 0.007 0.001 HIS B 509 PHE 0.018 0.001 PHE B 233 TYR 0.014 0.001 TYR B 383 ARG 0.008 0.000 ARG B 186 *********************** 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 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7910 (pp20) cc_final: 0.7338 (pm20) REVERT: A 713 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: B 232 GLU cc_start: 0.8129 (tp30) cc_final: 0.7870 (tp30) REVERT: B 318 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8373 (pt) REVERT: B 437 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 472 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7821 (mm-30) REVERT: B 501 PHE cc_start: 0.7846 (m-80) cc_final: 0.7494 (m-10) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.1756 time to fit residues: 26.7165 Evaluate side-chains 104 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 779 THR 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 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 437 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 30 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 238 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6576 Z= 0.190 Angle : 0.676 11.239 8882 Z= 0.326 Chirality : 0.043 0.141 996 Planarity : 0.004 0.078 1116 Dihedral : 4.290 18.892 854 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.48 % Allowed : 20.14 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.31), residues: 780 helix: 0.71 (0.29), residues: 333 sheet: -2.80 (0.62), residues: 67 loop : -1.00 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 356 HIS 0.006 0.001 HIS B 509 PHE 0.018 0.001 PHE B 233 TYR 0.014 0.001 TYR B 383 ARG 0.010 0.000 ARG B 186 *********************** 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 111 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7837 (tt0) cc_final: 0.7202 (pm20) REVERT: A 585 GLU cc_start: 0.7906 (pp20) cc_final: 0.7338 (pm20) REVERT: A 713 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: B 232 GLU cc_start: 0.8111 (tp30) cc_final: 0.7886 (tp30) REVERT: B 318 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (pt) REVERT: B 437 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8730 (tt) REVERT: B 472 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 501 PHE cc_start: 0.7836 (m-80) cc_final: 0.7509 (m-10) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.1666 time to fit residues: 24.3971 Evaluate side-chains 108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 437 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 77 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.0070 chunk 49 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 238 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6576 Z= 0.198 Angle : 0.687 11.240 8882 Z= 0.328 Chirality : 0.043 0.134 996 Planarity : 0.004 0.077 1116 Dihedral : 4.255 18.703 854 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.76 % Allowed : 19.86 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.31), residues: 780 helix: 0.71 (0.29), residues: 333 sheet: -2.72 (0.63), residues: 66 loop : -1.04 (0.34), residues: 381 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 0.017 0.001 PHE B 233 TYR 0.015 0.001 TYR A 460 ARG 0.011 0.000 ARG B 186 ********************** 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: 20 poor density : 94 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7911 (tt0) cc_final: 0.7126 (pm20) REVERT: A 441 ASP cc_start: 0.7969 (p0) cc_final: 0.7717 (p0) REVERT: A 585 GLU cc_start: 0.7864 (pp20) cc_final: 0.7330 (pm20) REVERT: A 627 LEU cc_start: 0.7595 (tt) cc_final: 0.7358 (tt) REVERT: A 713 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: B 232 GLU cc_start: 0.8101 (tp30) cc_final: 0.7410 (tp30) REVERT: B 236 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 318 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8382 (pt) REVERT: B 437 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 472 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 501 PHE cc_start: 0.7826 (m-80) cc_final: 0.7511 (m-10) outliers start: 20 outliers final: 14 residues processed: 105 average time/residue: 0.1699 time to fit residues: 24.4469 Evaluate side-chains 110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 656 MET 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 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 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 437 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 17 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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 238 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 = 0.4110 r_free = 0.4110 target = 0.155538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121846 restraints weight = 10768.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123166 restraints weight = 6941.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124792 restraints weight = 5162.560| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6576 Z= 0.170 Angle : 0.671 11.363 8882 Z= 0.318 Chirality : 0.042 0.138 996 Planarity : 0.004 0.074 1116 Dihedral : 4.153 18.329 854 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.76 % Allowed : 20.14 % Favored : 77.10 % 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: -0.60 (0.31), residues: 780 helix: 0.79 (0.29), residues: 333 sheet: -2.44 (0.66), residues: 61 loop : -1.09 (0.33), residues: 386 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 0.018 0.001 PHE B 448 TYR 0.014 0.001 TYR B 383 ARG 0.011 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.63 seconds wall clock time: 29 minutes 16.28 seconds (1756.28 seconds total)