Starting phenix.real_space_refine on Thu Feb 13 12:04:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp0_27627/02_2025/8dp0_27627.cif" } resolution = 2.96 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= -0.017 sd= 0.061 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 43 5.16 5 C 5699 2.51 5 N 1529 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7964 Classifications: {'peptide': 979} Link IDs: {'PTRANS': 46, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 930 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Time building chain proxies: 5.99, per 1000 atoms: 0.67 Number of scatterers: 8894 At special positions: 0 Unit cell: (87.98, 92.96, 107.9, 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 43 16.00 O 1623 8.00 N 1529 7.00 C 5699 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 46.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.119A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.540A pdb=" N GLN A 117 " --> pdb=" O GLN A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.097A pdb=" N GLY A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 332 " --> pdb=" O CYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 6.568A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.721A pdb=" N ARG A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 688 through 706 Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.503A pdb=" N PHE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 removed outlier: 3.641A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 798 through 801 Processing helix chain 'A' and resid 838 through 857 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.987A pdb=" N THR A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 915 removed outlier: 4.542A pdb=" N ASN A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 964 through 976 removed outlier: 3.820A pdb=" N ILE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.699A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.609A pdb=" N MET A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1055 removed outlier: 4.315A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1078 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.949A pdb=" N TRP B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 3.835A pdb=" N GLU A 55 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235 removed outlier: 7.145A pdb=" N PHE A 221 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 305 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 223 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 307 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS A 225 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.058A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.421A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 412 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 365 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 519 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 478 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 398 removed outlier: 6.734A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 429 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 465 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1200 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: 3.35 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2890 1.34 - 1.46: 1560 1.46 - 1.57: 4590 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 9105 Sorted by residual: bond pdb=" C ARG A 614 " pdb=" N GLU A 615 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.29e-02 6.01e+03 1.75e+00 bond pdb=" C ALA B 98 " pdb=" O ALA B 98 " ideal model delta sigma weight residual 1.243 1.234 0.010 9.50e-03 1.11e+04 1.07e+00 bond pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 1.469 1.481 -0.013 1.28e-02 6.10e+03 9.90e-01 bond pdb=" CB ILE A 643 " pdb=" CG2 ILE A 643 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.20e-01 bond pdb=" N GLY A 996 " pdb=" CA GLY A 996 " ideal model delta sigma weight residual 1.449 1.437 0.012 1.45e-02 4.76e+03 6.78e-01 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12135 1.56 - 3.13: 176 3.13 - 4.69: 21 4.69 - 6.25: 6 6.25 - 7.82: 3 Bond angle restraints: 12341 Sorted by residual: angle pdb=" C ALA B 98 " pdb=" CA ALA B 98 " pdb=" CB ALA B 98 " ideal model delta sigma weight residual 117.23 109.41 7.82 1.36e+00 5.41e-01 3.30e+01 angle pdb=" CA ALA B 98 " pdb=" C ALA B 98 " pdb=" N GLY B 99 " ideal model delta sigma weight residual 119.98 116.67 3.31 8.50e-01 1.38e+00 1.52e+01 angle pdb=" N VAL A 67 " pdb=" CA VAL A 67 " pdb=" C VAL A 67 " ideal model delta sigma weight residual 111.77 108.49 3.28 1.04e+00 9.25e-01 9.96e+00 angle pdb=" N ALA B 98 " pdb=" CA ALA B 98 " pdb=" C ALA B 98 " ideal model delta sigma weight residual 108.67 113.69 -5.02 1.67e+00 3.59e-01 9.05e+00 angle pdb=" N VAL A 326 " pdb=" CA VAL A 326 " pdb=" CB VAL A 326 " ideal model delta sigma weight residual 112.21 109.01 3.20 1.10e+00 8.26e-01 8.49e+00 ... (remaining 12336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4870 15.95 - 31.90: 456 31.90 - 47.85: 91 47.85 - 63.80: 22 63.80 - 79.75: 9 Dihedral angle restraints: 5448 sinusoidal: 2234 harmonic: 3214 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" CB ASP B 61 " pdb=" CG ASP B 61 " pdb=" OD1 ASP B 61 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASN B 96 " pdb=" C ASN B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N GLN A 69 " pdb=" CA GLN A 69 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 921 0.033 - 0.065: 302 0.065 - 0.098: 92 0.098 - 0.131: 48 0.131 - 0.164: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA THR A 182 " pdb=" N THR A 182 " pdb=" C THR A 182 " pdb=" CB THR A 182 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE A 643 " pdb=" CA ILE A 643 " pdb=" CG1 ILE A 643 " pdb=" CG2 ILE A 643 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 368 " pdb=" N ILE A 368 " pdb=" C ILE A 368 " pdb=" CB ILE A 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1363 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 547 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A 548 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 988 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 371 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.023 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 979 2.75 - 3.29: 8630 3.29 - 3.83: 14731 3.83 - 4.36: 17801 4.36 - 4.90: 30811 Nonbonded interactions: 72952 Sorted by model distance: nonbonded pdb=" OH TYR A1017 " pdb=" O ALA A1054 " model vdw 2.213 3.040 nonbonded pdb=" O TRP A 617 " pdb=" OG SER A 620 " model vdw 2.221 3.040 nonbonded pdb=" OE1 GLN A 705 " pdb=" OG SER A 871 " model vdw 2.268 3.040 nonbonded pdb=" O MET A1033 " pdb=" OG1 THR A1037 " model vdw 2.270 3.040 nonbonded pdb=" OE2 GLU A 384 " pdb=" NE2 GLN A 396 " model vdw 2.280 3.120 ... (remaining 72947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.002 0.030 9105 Z= 0.162 Angle : 0.500 7.818 12341 Z= 0.278 Chirality : 0.040 0.164 1366 Planarity : 0.004 0.070 1577 Dihedral : 13.313 79.755 3366 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1.09 (0.26), residues: 1088 helix: 1.71 (0.25), residues: 452 sheet: 0.23 (0.36), residues: 186 loop : 0.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 125 HIS 0.006 0.001 HIS A1023 PHE 0.011 0.001 PHE A 473 TYR 0.016 0.001 TYR A 110 ARG 0.007 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.973 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 1.1086 time to fit residues: 267.7403 Evaluate side-chains 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0470 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 959 ASN A1083 GLN B 32 ASN B 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075987 restraints weight = 17487.649| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.23 r_work: 0.2919 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9105 Z= 0.325 Angle : 0.718 9.657 12341 Z= 0.373 Chirality : 0.047 0.178 1366 Planarity : 0.005 0.062 1577 Dihedral : 4.511 17.315 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.40 % Allowed : 10.75 % Favored : 84.85 % 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: 0.47 (0.25), residues: 1088 helix: 1.13 (0.24), residues: 458 sheet: -0.14 (0.34), residues: 177 loop : -0.23 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 812 HIS 0.007 0.001 HIS B 50 PHE 0.014 0.002 PHE A 290 TYR 0.022 0.002 TYR A1067 ARG 0.007 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.946 Fit side-chains REVERT: A 366 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7700 (mtp85) REVERT: A 830 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8006 (mm) REVERT: A 995 MET cc_start: 0.8386 (mtm) cc_final: 0.8117 (mtp) REVERT: B 3 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7112 (pp30) REVERT: B 4 LEU cc_start: 0.8856 (mp) cc_final: 0.8645 (mp) REVERT: B 86 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7740 (mtpm) REVERT: B 118 GLN cc_start: 0.8946 (tp40) cc_final: 0.8515 (tp-100) outliers start: 43 outliers final: 10 residues processed: 133 average time/residue: 1.1333 time to fit residues: 162.7044 Evaluate side-chains 85 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 432 GLN A 735 GLN A 951 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074991 restraints weight = 17745.152| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.09 r_work: 0.2906 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9105 Z= 0.218 Angle : 0.545 10.505 12341 Z= 0.276 Chirality : 0.042 0.187 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.818 16.134 1185 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.56 % Allowed : 15.15 % Favored : 82.29 % 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 (0.25), residues: 1088 helix: 1.66 (0.24), residues: 459 sheet: 0.10 (0.35), residues: 186 loop : -0.19 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 812 HIS 0.006 0.001 HIS B 50 PHE 0.013 0.001 PHE A 578 TYR 0.013 0.001 TYR B 94 ARG 0.005 0.001 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.051 Fit side-chains REVERT: A 615 GLU cc_start: 0.7881 (tp30) cc_final: 0.7633 (tp30) REVERT: A 849 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8625 (mtm-85) REVERT: B 3 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7028 (pp30) REVERT: B 4 LEU cc_start: 0.8947 (mp) cc_final: 0.8680 (mp) REVERT: B 86 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7966 (mtmp) REVERT: B 88 GLU cc_start: 0.8626 (mp0) cc_final: 0.8423 (pm20) REVERT: B 118 GLN cc_start: 0.8925 (tp40) cc_final: 0.8553 (tp-100) outliers start: 25 outliers final: 8 residues processed: 96 average time/residue: 1.1229 time to fit residues: 116.6670 Evaluate side-chains 80 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070414 restraints weight = 17803.890| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.07 r_work: 0.2825 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 9105 Z= 0.348 Angle : 0.612 9.289 12341 Z= 0.309 Chirality : 0.044 0.226 1366 Planarity : 0.005 0.064 1577 Dihedral : 4.076 15.927 1185 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.58 % Allowed : 15.25 % Favored : 81.17 % 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: 0.78 (0.25), residues: 1088 helix: 1.53 (0.24), residues: 460 sheet: -0.04 (0.35), residues: 181 loop : -0.22 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 125 HIS 0.006 0.001 HIS B 50 PHE 0.014 0.002 PHE B 113 TYR 0.016 0.002 TYR A1067 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 1.246 Fit side-chains REVERT: A 239 ASP cc_start: 0.8155 (m-30) cc_final: 0.7816 (m-30) REVERT: A 707 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8402 (mtm180) REVERT: A 849 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8771 (mtm-85) REVERT: B 3 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7009 (pp30) REVERT: B 4 LEU cc_start: 0.9119 (mp) cc_final: 0.8886 (mp) REVERT: B 34 MET cc_start: 0.9088 (mmt) cc_final: 0.8844 (mmm) REVERT: B 86 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8066 (mtmp) REVERT: B 118 GLN cc_start: 0.9090 (tp40) cc_final: 0.8631 (tp-100) outliers start: 35 outliers final: 15 residues processed: 99 average time/residue: 1.0568 time to fit residues: 113.8570 Evaluate side-chains 77 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072269 restraints weight = 17582.062| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.03 r_work: 0.2879 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9105 Z= 0.231 Angle : 0.542 10.864 12341 Z= 0.271 Chirality : 0.042 0.206 1366 Planarity : 0.004 0.064 1577 Dihedral : 3.858 15.075 1185 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.35 % Allowed : 17.20 % Favored : 80.45 % 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: 0.98 (0.25), residues: 1088 helix: 1.76 (0.24), residues: 458 sheet: -0.03 (0.36), residues: 182 loop : -0.13 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE A 382 TYR 0.012 0.001 TYR A1067 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.010 Fit side-chains REVERT: A 239 ASP cc_start: 0.8204 (m-30) cc_final: 0.7901 (m-30) REVERT: A 849 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8917 (mtm-85) REVERT: A 1090 LEU cc_start: 0.8947 (tt) cc_final: 0.8542 (mm) REVERT: B 86 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8318 (mtmp) REVERT: B 118 GLN cc_start: 0.8973 (tp40) cc_final: 0.8621 (tp-100) outliers start: 23 outliers final: 15 residues processed: 88 average time/residue: 0.9889 time to fit residues: 95.2145 Evaluate side-chains 76 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073036 restraints weight = 17743.043| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.02 r_work: 0.2844 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9105 Z= 0.255 Angle : 0.545 10.792 12341 Z= 0.273 Chirality : 0.042 0.221 1366 Planarity : 0.004 0.064 1577 Dihedral : 3.839 14.958 1185 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.46 % Allowed : 18.22 % Favored : 79.32 % 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 (0.25), residues: 1088 helix: 1.79 (0.24), residues: 458 sheet: 0.01 (0.35), residues: 192 loop : -0.20 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 PHE 0.011 0.001 PHE A 382 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.938 Fit side-chains REVERT: A 239 ASP cc_start: 0.8087 (m-30) cc_final: 0.7610 (m-30) REVERT: A 849 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8759 (mtm-85) REVERT: A 1090 LEU cc_start: 0.8997 (tt) cc_final: 0.8544 (mm) REVERT: B 3 GLN cc_start: 0.8010 (pp30) cc_final: 0.7410 (pp30) REVERT: B 86 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8124 (mtmp) REVERT: B 118 GLN cc_start: 0.9078 (tp40) cc_final: 0.8615 (tp-100) outliers start: 24 outliers final: 14 residues processed: 81 average time/residue: 1.0376 time to fit residues: 91.8245 Evaluate side-chains 73 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 105 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072426 restraints weight = 17710.770| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.03 r_work: 0.2831 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9105 Z= 0.272 Angle : 0.543 10.396 12341 Z= 0.272 Chirality : 0.042 0.226 1366 Planarity : 0.004 0.064 1577 Dihedral : 3.862 15.059 1185 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 18.83 % Favored : 78.81 % 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: 0.96 (0.25), residues: 1088 helix: 1.79 (0.24), residues: 458 sheet: 0.01 (0.35), residues: 191 loop : -0.22 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 PHE 0.012 0.001 PHE A 382 TYR 0.013 0.001 TYR A1067 ARG 0.004 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.937 Fit side-chains REVERT: A 239 ASP cc_start: 0.8105 (m-30) cc_final: 0.7579 (m-30) REVERT: A 1039 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8721 (mmp) REVERT: A 1090 LEU cc_start: 0.8983 (tt) cc_final: 0.8463 (mm) REVERT: B 3 GLN cc_start: 0.7983 (pp30) cc_final: 0.7359 (pp30) REVERT: B 86 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8170 (mtmp) outliers start: 23 outliers final: 13 residues processed: 80 average time/residue: 1.0019 time to fit residues: 87.7349 Evaluate side-chains 74 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.0040 chunk 89 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074371 restraints weight = 17889.923| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.05 r_work: 0.2876 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9105 Z= 0.169 Angle : 0.514 11.909 12341 Z= 0.255 Chirality : 0.041 0.207 1366 Planarity : 0.004 0.063 1577 Dihedral : 3.652 14.371 1185 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 19.24 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1088 helix: 1.93 (0.24), residues: 459 sheet: 0.06 (0.35), residues: 192 loop : -0.13 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 29 TYR 0.011 0.001 TYR A1067 ARG 0.008 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.974 Fit side-chains REVERT: A 1039 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8851 (mmp) REVERT: A 1090 LEU cc_start: 0.8979 (tt) cc_final: 0.8465 (mm) REVERT: B 3 GLN cc_start: 0.7898 (pp30) cc_final: 0.7259 (pp30) REVERT: B 34 MET cc_start: 0.9174 (mmt) cc_final: 0.8866 (mmm) REVERT: B 86 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8179 (mtmp) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.9272 time to fit residues: 82.5249 Evaluate side-chains 73 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073867 restraints weight = 17606.259| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.06 r_work: 0.2897 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.7977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9105 Z= 0.155 Angle : 0.513 11.548 12341 Z= 0.254 Chirality : 0.041 0.208 1366 Planarity : 0.004 0.070 1577 Dihedral : 3.598 13.759 1185 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 19.65 % Favored : 78.71 % 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: 1.19 (0.26), residues: 1088 helix: 2.02 (0.24), residues: 459 sheet: 0.07 (0.35), residues: 192 loop : -0.13 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.013 0.001 PHE A 42 TYR 0.010 0.001 TYR A 720 ARG 0.020 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.061 Fit side-chains REVERT: A 1039 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8852 (mmp) REVERT: A 1090 LEU cc_start: 0.8956 (tt) cc_final: 0.8431 (mm) REVERT: B 3 GLN cc_start: 0.7863 (pp30) cc_final: 0.7226 (pp30) REVERT: B 34 MET cc_start: 0.9150 (mmt) cc_final: 0.8829 (mmm) REVERT: B 86 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8143 (mtmp) REVERT: B 123 THR cc_start: 0.9124 (t) cc_final: 0.8795 (p) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.9488 time to fit residues: 83.6337 Evaluate side-chains 77 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.070317 restraints weight = 17823.755| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.07 r_work: 0.2816 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.8141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9105 Z= 0.308 Angle : 0.570 10.503 12341 Z= 0.286 Chirality : 0.043 0.250 1366 Planarity : 0.005 0.080 1577 Dihedral : 3.855 15.003 1185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.33 % Allowed : 20.68 % Favored : 77.99 % 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 (0.25), residues: 1088 helix: 1.89 (0.24), residues: 458 sheet: 0.01 (0.34), residues: 192 loop : -0.26 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 125 HIS 0.006 0.001 HIS B 50 PHE 0.012 0.001 PHE A 382 TYR 0.015 0.001 TYR A1067 ARG 0.019 0.001 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.085 Fit side-chains REVERT: A 130 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8194 (mtp85) REVERT: A 798 ILE cc_start: 0.7752 (pt) cc_final: 0.7475 (mt) REVERT: A 1039 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8803 (mmp) REVERT: B 3 GLN cc_start: 0.7901 (pp30) cc_final: 0.7284 (pp30) REVERT: B 86 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8151 (mtmp) REVERT: B 123 THR cc_start: 0.9170 (t) cc_final: 0.8848 (p) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 1.0770 time to fit residues: 89.6062 Evaluate side-chains 72 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071413 restraints weight = 17663.007| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.06 r_work: 0.2846 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.8246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9105 Z= 0.232 Angle : 0.551 10.424 12341 Z= 0.273 Chirality : 0.042 0.212 1366 Planarity : 0.004 0.076 1577 Dihedral : 3.787 15.353 1185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.43 % Allowed : 20.57 % Favored : 77.99 % 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: 1.04 (0.25), residues: 1088 helix: 1.95 (0.24), residues: 456 sheet: 0.01 (0.34), residues: 192 loop : -0.27 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE A 382 TYR 0.013 0.001 TYR A1067 ARG 0.019 0.001 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.09 seconds wall clock time: 93 minutes 14.56 seconds (5594.56 seconds total)