Starting phenix.real_space_refine on Sat Aug 23 01:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dp0_27627/08_2025/8dp0_27627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp0_27627/08_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_27627/08_2025/8dp0_27627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp0_27627/08_2025/8dp0_27627.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp0_27627/08_2025/8dp0_27627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp0_27627/08_2025/8dp0_27627.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.27 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: 0.84 Conformation dependent library (CDL) restraints added in 265.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.41 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: 1.91 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 4.570 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.060 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- 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= 0.115 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG A 552 TYR 0.016 0.001 TYR A 110 PHE 0.011 0.001 PHE A 473 TRP 0.020 0.001 TRP A 125 HIS 0.006 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9105) covalent geometry : angle 0.50014 (12341) hydrogen bonds : bond 0.16027 ( 424) hydrogen bonds : angle 5.85796 ( 1200) *********************** 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 : 0.374 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.4423 time to fit residues: 106.8623 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 : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 705 GLN A 735 GLN A 959 ASN A1083 GLN B 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077028 restraints weight = 17325.493| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.17 r_work: 0.2992 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9105 Z= 0.148 Angle : 0.617 8.632 12341 Z= 0.317 Chirality : 0.043 0.159 1366 Planarity : 0.005 0.059 1577 Dihedral : 3.865 15.050 1185 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.87 % Allowed : 12.59 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1088 helix: 1.59 (0.24), residues: 457 sheet: 0.16 (0.36), residues: 175 loop : -0.03 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 184 TYR 0.019 0.002 TYR A1067 PHE 0.014 0.001 PHE A 175 TRP 0.016 0.002 TRP A 812 HIS 0.006 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9105) covalent geometry : angle 0.61662 (12341) hydrogen bonds : bond 0.03602 ( 424) hydrogen bonds : angle 4.32873 ( 1200) *********************** 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 157 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7574 (mtp85) REVERT: A 559 ILE cc_start: 0.8591 (mt) cc_final: 0.8309 (mp) REVERT: A 679 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8496 (mtt-85) REVERT: A 1049 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: B 3 GLN cc_start: 0.7747 (tm-30) cc_final: 0.7158 (pp30) outliers start: 28 outliers final: 8 residues processed: 147 average time/residue: 0.3731 time to fit residues: 59.6707 Evaluate side-chains 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 16 optimal weight: 0.0040 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 512 ASN A 951 ASN B 83 ASN B 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073433 restraints weight = 17594.939| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.27 r_work: 0.2887 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9105 Z= 0.170 Angle : 0.632 10.479 12341 Z= 0.318 Chirality : 0.045 0.171 1366 Planarity : 0.005 0.059 1577 Dihedral : 3.924 15.047 1185 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.79 % Allowed : 14.94 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1088 helix: 1.49 (0.24), residues: 460 sheet: 0.01 (0.36), residues: 181 loop : -0.12 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 130 TYR 0.017 0.002 TYR B 37 PHE 0.014 0.002 PHE B 29 TRP 0.016 0.002 TRP A 812 HIS 0.007 0.001 HIS A 967 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9105) covalent geometry : angle 0.63219 (12341) hydrogen bonds : bond 0.04538 ( 424) hydrogen bonds : angle 4.30979 ( 1200) *********************** 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 125 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.270 Fit side-chains REVERT: A 282 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8557 (m) REVERT: A 550 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8408 (mp10) REVERT: A 849 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8461 (mtm-85) REVERT: B 3 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7046 (pp30) REVERT: B 4 LEU cc_start: 0.8909 (mp) cc_final: 0.8696 (mp) REVERT: B 86 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7855 (mtmp) outliers start: 37 outliers final: 10 residues processed: 114 average time/residue: 0.4097 time to fit residues: 50.6171 Evaluate side-chains 82 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.073142 restraints weight = 17956.947| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.12 r_work: 0.2858 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 9105 Z= 0.172 Angle : 0.560 10.232 12341 Z= 0.281 Chirality : 0.043 0.198 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.838 15.462 1185 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.07 % Allowed : 16.58 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1088 helix: 1.71 (0.24), residues: 459 sheet: 0.01 (0.36), residues: 181 loop : -0.01 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.012 0.001 TYR B 94 PHE 0.012 0.001 PHE A 382 TRP 0.028 0.002 TRP A 125 HIS 0.006 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9105) covalent geometry : angle 0.55993 (12341) hydrogen bonds : bond 0.03679 ( 424) hydrogen bonds : angle 4.05961 ( 1200) *********************** 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: 30 poor density : 74 time to evaluate : 0.239 Fit side-chains REVERT: A 239 ASP cc_start: 0.8025 (m-30) cc_final: 0.7666 (m-30) REVERT: A 550 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8476 (mp10) REVERT: A 849 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (mtm-85) REVERT: B 3 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7051 (pp30) REVERT: B 4 LEU cc_start: 0.8985 (mp) cc_final: 0.8738 (mp) REVERT: B 86 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8044 (mtmp) outliers start: 30 outliers final: 9 residues processed: 96 average time/residue: 0.3985 time to fit residues: 41.8171 Evaluate side-chains 75 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 460 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 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 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 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.072572 restraints weight = 17583.317| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.09 r_work: 0.2879 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9105 Z= 0.142 Angle : 0.533 10.186 12341 Z= 0.266 Chirality : 0.042 0.225 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.721 14.944 1185 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.87 % Allowed : 16.58 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1088 helix: 1.78 (0.24), residues: 459 sheet: -0.08 (0.36), residues: 181 loop : -0.00 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 130 TYR 0.010 0.001 TYR A 720 PHE 0.011 0.001 PHE A 382 TRP 0.034 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9105) covalent geometry : angle 0.53250 (12341) hydrogen bonds : bond 0.03607 ( 424) hydrogen bonds : angle 3.98717 ( 1200) *********************** 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 102 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.314 Fit side-chains REVERT: A 239 ASP cc_start: 0.7976 (m-30) cc_final: 0.7702 (m-30) REVERT: A 849 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (mtm-85) REVERT: A 960 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 1090 LEU cc_start: 0.8957 (tt) cc_final: 0.8522 (mm) REVERT: B 3 GLN cc_start: 0.7649 (tm-30) cc_final: 0.6956 (pp30) REVERT: B 4 LEU cc_start: 0.9066 (mp) cc_final: 0.8746 (mp) REVERT: B 86 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8116 (mtmp) outliers start: 28 outliers final: 11 residues processed: 95 average time/residue: 0.3765 time to fit residues: 39.0663 Evaluate side-chains 78 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 460 LEU 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 960 LEU Chi-restraints excluded: chain A residue 961 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.102595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073891 restraints weight = 17755.211| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.05 r_work: 0.2889 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9105 Z= 0.138 Angle : 0.532 10.052 12341 Z= 0.265 Chirality : 0.042 0.221 1366 Planarity : 0.004 0.063 1577 Dihedral : 3.700 14.760 1185 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.46 % Allowed : 17.81 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1088 helix: 1.83 (0.24), residues: 459 sheet: -0.08 (0.36), residues: 181 loop : -0.01 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.010 0.001 TYR A 720 PHE 0.012 0.001 PHE A 382 TRP 0.037 0.001 TRP A 125 HIS 0.007 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9105) covalent geometry : angle 0.53237 (12341) hydrogen bonds : bond 0.03513 ( 424) hydrogen bonds : angle 3.97903 ( 1200) *********************** 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 92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.358 Fit side-chains REVERT: A 239 ASP cc_start: 0.8050 (m-30) cc_final: 0.7751 (m-30) REVERT: A 849 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8913 (mtm-85) REVERT: A 960 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8916 (tt) REVERT: A 1090 LEU cc_start: 0.8942 (tt) cc_final: 0.8520 (mm) REVERT: B 3 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7115 (pp30) REVERT: B 4 LEU cc_start: 0.9107 (mp) cc_final: 0.8800 (mp) REVERT: B 86 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8258 (mtmp) outliers start: 24 outliers final: 9 residues processed: 88 average time/residue: 0.4142 time to fit residues: 39.9503 Evaluate side-chains 75 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 333 THR 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 A residue 992 LEU Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 91 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074365 restraints weight = 17930.796| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.10 r_work: 0.2890 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9105 Z= 0.105 Angle : 0.509 10.771 12341 Z= 0.251 Chirality : 0.041 0.214 1366 Planarity : 0.004 0.061 1577 Dihedral : 3.585 14.421 1185 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.15 % Allowed : 19.24 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.26), residues: 1088 helix: 1.92 (0.24), residues: 460 sheet: -0.02 (0.37), residues: 182 loop : 0.05 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.010 0.001 TYR A 720 PHE 0.011 0.001 PHE B 29 TRP 0.016 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9105) covalent geometry : angle 0.50884 (12341) hydrogen bonds : bond 0.03177 ( 424) hydrogen bonds : angle 3.88486 ( 1200) *********************** 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 89 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.388 Fit side-chains REVERT: A 239 ASP cc_start: 0.7879 (m-30) cc_final: 0.7530 (m-30) REVERT: A 1049 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: A 1090 LEU cc_start: 0.8964 (tt) cc_final: 0.8463 (mm) REVERT: B 3 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7035 (pp30) REVERT: B 4 LEU cc_start: 0.9076 (mp) cc_final: 0.8768 (mp) REVERT: B 86 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8096 (mtmp) outliers start: 21 outliers final: 13 residues processed: 85 average time/residue: 0.4182 time to fit residues: 38.9451 Evaluate side-chains 77 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 620 SER 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 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.101815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073171 restraints weight = 17715.269| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.15 r_work: 0.2868 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9105 Z= 0.119 Angle : 0.528 10.350 12341 Z= 0.260 Chirality : 0.041 0.208 1366 Planarity : 0.004 0.061 1577 Dihedral : 3.589 15.705 1185 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.84 % Allowed : 20.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1088 helix: 1.91 (0.24), residues: 460 sheet: 0.10 (0.35), residues: 202 loop : -0.05 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 849 TYR 0.019 0.001 TYR A 462 PHE 0.011 0.001 PHE B 29 TRP 0.033 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9105) covalent geometry : angle 0.52841 (12341) hydrogen bonds : bond 0.03255 ( 424) hydrogen bonds : angle 3.90520 ( 1200) *********************** 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 83 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.358 Fit side-chains REVERT: A 239 ASP cc_start: 0.7877 (m-30) cc_final: 0.7518 (m-30) REVERT: A 1049 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: B 3 GLN cc_start: 0.7660 (tm-30) cc_final: 0.6988 (pp30) REVERT: B 4 LEU cc_start: 0.9032 (mp) cc_final: 0.8739 (mp) REVERT: B 86 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8027 (mtmp) outliers start: 18 outliers final: 16 residues processed: 79 average time/residue: 0.3881 time to fit residues: 33.6409 Evaluate side-chains 81 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 GLN 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 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN B 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072613 restraints weight = 17706.974| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.02 r_work: 0.2873 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9105 Z= 0.152 Angle : 0.550 10.437 12341 Z= 0.272 Chirality : 0.042 0.238 1366 Planarity : 0.004 0.061 1577 Dihedral : 3.724 20.087 1185 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 19.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.26), residues: 1088 helix: 1.85 (0.24), residues: 460 sheet: 0.10 (0.36), residues: 192 loop : -0.05 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 849 TYR 0.015 0.001 TYR A 462 PHE 0.012 0.001 PHE A 382 TRP 0.017 0.001 TRP A 125 HIS 0.008 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9105) covalent geometry : angle 0.54960 (12341) hydrogen bonds : bond 0.03588 ( 424) hydrogen bonds : angle 4.04427 ( 1200) *********************** 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 91 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.349 Fit side-chains REVERT: A 140 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8722 (ttp-110) REVERT: A 1049 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: A 1090 LEU cc_start: 0.8950 (tt) cc_final: 0.8423 (mm) REVERT: B 86 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8287 (mtmp) outliers start: 21 outliers final: 12 residues processed: 87 average time/residue: 0.4110 time to fit residues: 38.7644 Evaluate side-chains 78 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 26 optimal weight: 0.0570 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.102148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073478 restraints weight = 17716.055| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.02 r_work: 0.2894 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.8098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9105 Z= 0.117 Angle : 0.551 10.538 12341 Z= 0.271 Chirality : 0.042 0.225 1366 Planarity : 0.004 0.071 1577 Dihedral : 3.673 16.720 1185 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 20.88 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1088 helix: 1.80 (0.24), residues: 466 sheet: 0.22 (0.37), residues: 182 loop : -0.07 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 130 TYR 0.014 0.001 TYR A 462 PHE 0.011 0.001 PHE A 961 TRP 0.036 0.001 TRP A 125 HIS 0.006 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9105) covalent geometry : angle 0.55074 (12341) hydrogen bonds : bond 0.03274 ( 424) hydrogen bonds : angle 3.97296 ( 1200) ********************** 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 84 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.395 Fit side-chains REVERT: A 140 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8727 (ttp-110) REVERT: A 1049 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: A 1090 LEU cc_start: 0.8950 (tt) cc_final: 0.8427 (mm) REVERT: B 3 GLN cc_start: 0.8008 (pp30) cc_final: 0.7566 (pp30) REVERT: B 86 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8294 (mtmp) REVERT: B 88 GLU cc_start: 0.8137 (pm20) cc_final: 0.7935 (mp0) REVERT: B 123 THR cc_start: 0.9271 (t) cc_final: 0.8971 (p) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.4297 time to fit residues: 37.4880 Evaluate side-chains 78 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073153 restraints weight = 17498.303| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.03 r_work: 0.2883 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9105 Z= 0.132 Angle : 0.553 10.086 12341 Z= 0.273 Chirality : 0.042 0.238 1366 Planarity : 0.004 0.088 1577 Dihedral : 3.658 14.576 1185 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.64 % Allowed : 21.29 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1088 helix: 1.86 (0.24), residues: 461 sheet: 0.19 (0.36), residues: 181 loop : -0.07 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 130 TYR 0.014 0.001 TYR A 462 PHE 0.013 0.001 PHE B 113 TRP 0.043 0.001 TRP A 125 HIS 0.007 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9105) covalent geometry : angle 0.55322 (12341) hydrogen bonds : bond 0.03407 ( 424) hydrogen bonds : angle 4.01534 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.24 seconds wall clock time: 38 minutes 7.95 seconds (2287.95 seconds total)