Starting phenix.real_space_refine on Tue Feb 3 21:59:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.map" model { file = "/net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n87_49117/02_2026/9n87_49117.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 50 5.16 5 C 4525 2.51 5 N 1225 2.21 5 O 1395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7195 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6805 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 838} Chain: "B" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 390 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Time building chain proxies: 1.76, per 1000 atoms: 0.24 Number of scatterers: 7195 At special positions: 0 Unit cell: (95.92, 91.56, 114.232, 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 50 16.00 O 1395 8.00 N 1225 7.00 C 4525 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: 0.75 Conformation dependent library (CDL) restraints added in 282.5 milliseconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.535A pdb=" N LEU A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 22 Processing helix chain 'A' and resid 22 through 29 removed outlier: 4.009A pdb=" N GLU A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.736A pdb=" N LEU A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.921A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.242A pdb=" N LYS A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.725A pdb=" N LEU A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.568A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.908A pdb=" N GLN A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 168 " --> pdb=" O GLN A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 168' Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.600A pdb=" N ASN A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.574A pdb=" N ARG A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.833A pdb=" N GLU A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 254 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.509A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 removed outlier: 3.663A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A 287 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.578A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.621A pdb=" N HIS A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.564A pdb=" N ILE A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.623A pdb=" N CYS A 392 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 417 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 404 - end of helix Proline residue: A 411 - end of helix removed outlier: 3.570A pdb=" N GLU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 463 through 471 removed outlier: 4.438A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 499 through 515 removed outlier: 4.523A pdb=" N GLU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.536A pdb=" N VAL A 547 " --> pdb=" O CYS A 543 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.954A pdb=" N LEU A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.163A pdb=" N GLU A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 removed outlier: 4.130A pdb=" N GLU A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Proline residue: A 652 - end of helix removed outlier: 3.951A pdb=" N LYS A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 removed outlier: 3.506A pdb=" N CYS A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.523A pdb=" N ALA A 680 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 3.671A pdb=" N VAL A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 4.310A pdb=" N GLN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 4.155A pdb=" N ASN A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR A 738 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 778 Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.664A pdb=" N LEU A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Proline residue: A 792 - end of helix Processing helix chain 'A' and resid 793 through 807 removed outlier: 3.906A pdb=" N ASP A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 841 through 851 removed outlier: 3.942A pdb=" N GLU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 removed outlier: 3.635A pdb=" N LEU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 42 removed outlier: 3.681A pdb=" N ALA B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' 419 hydrogen bonds defined for protein. 1236 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: 1.11 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2442 1.34 - 1.46: 1378 1.46 - 1.58: 3417 1.58 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7313 Sorted by residual: bond pdb=" C ILE A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 1.335 1.344 -0.010 1.19e-02 7.06e+03 6.81e-01 bond pdb=" CA LYS A 651 " pdb=" C LYS A 651 " ideal model delta sigma weight residual 1.525 1.534 -0.009 1.19e-02 7.06e+03 6.12e-01 bond pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 bond pdb=" CA ILE A 121 " pdb=" C ILE A 121 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.05e-02 9.07e+03 5.99e-01 bond pdb=" CA GLN A 227 " pdb=" C GLN A 227 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.63e-01 ... (remaining 7308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 9773 1.88 - 3.76: 120 3.76 - 5.63: 23 5.63 - 7.51: 3 7.51 - 9.39: 1 Bond angle restraints: 9920 Sorted by residual: angle pdb=" C ALA A 87 " pdb=" N ARG A 88 " pdb=" CA ARG A 88 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C VAL A 242 " pdb=" N LYS A 243 " pdb=" CA LYS A 243 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" CA LEU A 44 " pdb=" CB LEU A 44 " pdb=" CG LEU A 44 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" C GLY A 623 " pdb=" N VAL A 624 " pdb=" CA VAL A 624 " ideal model delta sigma weight residual 123.16 120.45 2.71 1.06e+00 8.90e-01 6.54e+00 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 109.34 114.28 -4.94 2.08e+00 2.31e-01 5.63e+00 ... (remaining 9915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4155 17.80 - 35.59: 275 35.59 - 53.39: 79 53.39 - 71.19: 5 71.19 - 88.98: 7 Dihedral angle restraints: 4521 sinusoidal: 1813 harmonic: 2708 Sorted by residual: dihedral pdb=" CA LYS A 243 " pdb=" C LYS A 243 " pdb=" N ILE A 244 " pdb=" CA ILE A 244 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA VAL A 470 " pdb=" C VAL A 470 " pdb=" N CYS A 471 " pdb=" CA CYS A 471 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TRP A 472 " pdb=" C TRP A 472 " pdb=" N ALA A 473 " pdb=" CA ALA A 473 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 738 0.033 - 0.066: 319 0.066 - 0.098: 73 0.098 - 0.131: 17 0.131 - 0.164: 2 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA LYS A 651 " pdb=" N LYS A 651 " pdb=" C LYS A 651 " pdb=" CB LYS A 651 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CB ILE A 121 " pdb=" CA ILE A 121 " pdb=" CG1 ILE A 121 " pdb=" CG2 ILE A 121 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA CYS A 543 " pdb=" N CYS A 543 " pdb=" C CYS A 543 " pdb=" CB CYS A 543 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1146 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 88 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C ARG A 88 " -0.077 2.00e-02 2.50e+03 pdb=" O ARG A 88 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 89 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 764 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C SER A 764 " 0.025 2.00e-02 2.50e+03 pdb=" O SER A 764 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 765 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 8 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " 0.019 5.00e-02 4.00e+02 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1534 2.78 - 3.31: 7964 3.31 - 3.84: 11654 3.84 - 4.37: 13423 4.37 - 4.90: 22076 Nonbonded interactions: 56651 Sorted by model distance: nonbonded pdb=" O LYS A 62 " pdb=" OG1 THR A 66 " model vdw 2.248 3.040 nonbonded pdb=" O GLN A 548 " pdb=" OG1 THR A 551 " model vdw 2.252 3.040 nonbonded pdb=" O ALA A 409 " pdb=" OG1 THR A 412 " model vdw 2.356 3.040 nonbonded pdb=" O SER A 475 " pdb=" OG SER A 476 " model vdw 2.359 3.040 nonbonded pdb=" O TYR A 497 " pdb=" OG SER A 500 " model vdw 2.362 3.040 ... (remaining 56646 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: 1.130 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.027 7313 Z= 0.117 Angle : 0.571 9.391 9920 Z= 0.303 Chirality : 0.037 0.164 1149 Planarity : 0.004 0.044 1297 Dihedral : 13.097 88.985 2757 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.02 % Allowed : 9.58 % Favored : 88.40 % 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 are not related in a simple way. whole: 0.42 (0.28), residues: 917 helix: 0.54 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.015 0.001 TYR A 497 PHE 0.010 0.001 PHE A 217 TRP 0.012 0.001 TRP A 430 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7313) covalent geometry : angle 0.57071 ( 9920) hydrogen bonds : bond 0.16706 ( 419) hydrogen bonds : angle 5.25937 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5570 (tpt) cc_final: 0.5164 (tpt) REVERT: A 296 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8265 (tm-30) REVERT: A 661 TYR cc_start: 0.8724 (p90) cc_final: 0.8364 (p90) REVERT: A 693 MET cc_start: 0.9042 (mmm) cc_final: 0.8788 (mmt) REVERT: A 770 THR cc_start: 0.9010 (p) cc_final: 0.8580 (p) REVERT: A 842 MET cc_start: 0.8420 (mtp) cc_final: 0.7844 (ttt) REVERT: B 1 MET cc_start: 0.0706 (tpp) cc_final: 0.0504 (tpp) REVERT: B 27 GLN cc_start: 0.7473 (tm-30) cc_final: 0.6701 (tm-30) outliers start: 16 outliers final: 3 residues processed: 141 average time/residue: 0.1009 time to fit residues: 18.7870 Evaluate side-chains 88 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 244 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 196 ASN A 208 ASN A 239 GLN A 278 GLN A 328 GLN A 401 GLN A 560 GLN A 684 ASN A 780 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.102927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075606 restraints weight = 25762.876| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 5.10 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7313 Z= 0.165 Angle : 0.671 10.167 9920 Z= 0.335 Chirality : 0.042 0.174 1149 Planarity : 0.004 0.047 1297 Dihedral : 4.921 33.204 994 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.28 % Allowed : 12.86 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 917 helix: 0.77 (0.21), residues: 652 sheet: None (None), residues: 0 loop : 0.19 (0.43), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 613 TYR 0.026 0.002 TYR A 255 PHE 0.016 0.002 PHE A 217 TRP 0.028 0.002 TRP A 126 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7313) covalent geometry : angle 0.67103 ( 9920) hydrogen bonds : bond 0.04873 ( 419) hydrogen bonds : angle 4.62585 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.9006 (mt) cc_final: 0.8753 (pp) REVERT: A 181 MET cc_start: 0.5681 (tpt) cc_final: 0.5251 (tpt) REVERT: A 196 ASN cc_start: 0.9183 (m-40) cc_final: 0.8814 (m110) REVERT: A 250 GLN cc_start: 0.8923 (mp10) cc_final: 0.8650 (pm20) REVERT: A 296 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8223 (tm-30) REVERT: A 319 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 388 MET cc_start: 0.8571 (tpt) cc_final: 0.7758 (tpt) REVERT: A 614 MET cc_start: 0.9552 (ppp) cc_final: 0.9338 (ppp) REVERT: A 626 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: A 627 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8959 (p0) REVERT: A 661 TYR cc_start: 0.8728 (p90) cc_final: 0.8370 (p90) REVERT: A 684 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7823 (t0) REVERT: A 693 MET cc_start: 0.9063 (mmm) cc_final: 0.8851 (mmt) REVERT: A 760 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8835 (mm-30) REVERT: A 767 GLU cc_start: 0.8725 (tp30) cc_final: 0.8425 (pp20) REVERT: A 842 MET cc_start: 0.8337 (mtp) cc_final: 0.7588 (mpp) REVERT: A 845 GLU cc_start: 0.9042 (pt0) cc_final: 0.8237 (tm-30) outliers start: 26 outliers final: 9 residues processed: 112 average time/residue: 0.0758 time to fit residues: 11.9627 Evaluate side-chains 95 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 25 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.103483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.075489 restraints weight = 25878.317| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 5.04 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7313 Z= 0.141 Angle : 0.631 9.004 9920 Z= 0.310 Chirality : 0.041 0.199 1149 Planarity : 0.004 0.054 1297 Dihedral : 4.802 37.689 994 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.40 % Allowed : 15.38 % Favored : 81.21 % 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 are not related in a simple way. whole: 0.83 (0.29), residues: 917 helix: 0.81 (0.21), residues: 657 sheet: None (None), residues: 0 loop : 0.17 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 613 TYR 0.012 0.001 TYR A 497 PHE 0.016 0.001 PHE A 217 TRP 0.021 0.002 TRP A 126 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7313) covalent geometry : angle 0.63111 ( 9920) hydrogen bonds : bond 0.04228 ( 419) hydrogen bonds : angle 4.43437 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8993 (mt) cc_final: 0.8746 (pp) REVERT: A 181 MET cc_start: 0.5700 (tpt) cc_final: 0.4955 (tpt) REVERT: A 196 ASN cc_start: 0.9333 (m-40) cc_final: 0.8959 (m110) REVERT: A 296 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8241 (tm-30) REVERT: A 319 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 627 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (p0) REVERT: A 661 TYR cc_start: 0.8611 (p90) cc_final: 0.8244 (p90) REVERT: A 767 GLU cc_start: 0.8728 (tp30) cc_final: 0.8347 (pp20) REVERT: A 842 MET cc_start: 0.8275 (mtp) cc_final: 0.7911 (ttt) REVERT: A 845 GLU cc_start: 0.8976 (pt0) cc_final: 0.8637 (tm-30) REVERT: A 870 ARG cc_start: 0.9131 (ptp90) cc_final: 0.8913 (tpp-160) REVERT: B 27 GLN cc_start: 0.8280 (tm-30) cc_final: 0.6875 (tm-30) REVERT: B 31 GLU cc_start: 0.9336 (tt0) cc_final: 0.9115 (mm-30) outliers start: 27 outliers final: 13 residues processed: 106 average time/residue: 0.0799 time to fit residues: 11.9099 Evaluate side-chains 95 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.104544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.076461 restraints weight = 26063.240| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 5.13 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7313 Z= 0.117 Angle : 0.619 10.351 9920 Z= 0.300 Chirality : 0.040 0.186 1149 Planarity : 0.004 0.053 1297 Dihedral : 4.456 30.519 992 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.03 % Allowed : 16.65 % Favored : 80.33 % 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 are not related in a simple way. whole: 1.03 (0.29), residues: 917 helix: 1.00 (0.21), residues: 646 sheet: None (None), residues: 0 loop : 0.17 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 613 TYR 0.012 0.001 TYR A 76 PHE 0.017 0.001 PHE A 217 TRP 0.013 0.001 TRP A 126 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7313) covalent geometry : angle 0.61922 ( 9920) hydrogen bonds : bond 0.03786 ( 419) hydrogen bonds : angle 4.24132 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8987 (mt) cc_final: 0.8735 (pp) REVERT: A 148 GLU cc_start: 0.7728 (pt0) cc_final: 0.6514 (pp20) REVERT: A 181 MET cc_start: 0.5714 (tpt) cc_final: 0.5011 (tpt) REVERT: A 196 ASN cc_start: 0.9348 (m-40) cc_final: 0.8987 (m110) REVERT: A 296 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8241 (tm-30) REVERT: A 319 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (mm) REVERT: A 355 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9231 (mp) REVERT: A 627 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8768 (p0) REVERT: A 661 TYR cc_start: 0.8632 (p90) cc_final: 0.8272 (p90) REVERT: A 767 GLU cc_start: 0.8732 (tp30) cc_final: 0.8312 (pp20) REVERT: A 842 MET cc_start: 0.8222 (mtp) cc_final: 0.7868 (ttt) REVERT: A 845 GLU cc_start: 0.8937 (pt0) cc_final: 0.8625 (tm-30) REVERT: A 870 ARG cc_start: 0.9118 (ptp90) cc_final: 0.8900 (tpp-160) REVERT: B 31 GLU cc_start: 0.9301 (tt0) cc_final: 0.8902 (tp30) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 0.0685 time to fit residues: 10.4046 Evaluate side-chains 96 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075306 restraints weight = 25593.956| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.93 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7313 Z= 0.143 Angle : 0.629 10.477 9920 Z= 0.308 Chirality : 0.041 0.181 1149 Planarity : 0.004 0.053 1297 Dihedral : 4.397 26.943 992 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.66 % Allowed : 17.65 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 917 helix: 1.02 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 762 TYR 0.030 0.002 TYR A 76 PHE 0.007 0.001 PHE A 650 TRP 0.009 0.001 TRP A 430 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7313) covalent geometry : angle 0.62882 ( 9920) hydrogen bonds : bond 0.03844 ( 419) hydrogen bonds : angle 4.27881 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5727 (tpt) cc_final: 0.5208 (tpt) REVERT: A 196 ASN cc_start: 0.9345 (m-40) cc_final: 0.8967 (m110) REVERT: A 296 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8208 (tm-30) REVERT: A 319 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 355 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9260 (mp) REVERT: A 627 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.8796 (p0) REVERT: A 661 TYR cc_start: 0.8667 (p90) cc_final: 0.8321 (p90) REVERT: A 766 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 767 GLU cc_start: 0.8707 (tp30) cc_final: 0.8333 (pp20) REVERT: A 842 MET cc_start: 0.8274 (mtp) cc_final: 0.7931 (ttt) REVERT: A 845 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: A 870 ARG cc_start: 0.9118 (ptp90) cc_final: 0.8892 (tpp-160) outliers start: 29 outliers final: 17 residues processed: 107 average time/residue: 0.0786 time to fit residues: 11.9649 Evaluate side-chains 98 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.103283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.075111 restraints weight = 26320.555| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 5.16 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7313 Z= 0.133 Angle : 0.636 11.326 9920 Z= 0.306 Chirality : 0.041 0.197 1149 Planarity : 0.004 0.050 1297 Dihedral : 4.289 23.511 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 18.92 % Favored : 78.18 % 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 are not related in a simple way. whole: 1.04 (0.29), residues: 917 helix: 1.06 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 762 TYR 0.040 0.002 TYR A 76 PHE 0.017 0.001 PHE A 217 TRP 0.008 0.001 TRP A 430 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7313) covalent geometry : angle 0.63633 ( 9920) hydrogen bonds : bond 0.03692 ( 419) hydrogen bonds : angle 4.24295 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5834 (tpt) cc_final: 0.5222 (tpt) REVERT: A 196 ASN cc_start: 0.9372 (m-40) cc_final: 0.8996 (m110) REVERT: A 296 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8213 (tm-30) REVERT: A 319 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 355 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9243 (mp) REVERT: A 627 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8827 (p0) REVERT: A 661 TYR cc_start: 0.8634 (p90) cc_final: 0.8297 (p90) REVERT: A 766 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 767 GLU cc_start: 0.8748 (tp30) cc_final: 0.8332 (pp20) REVERT: A 845 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: A 870 ARG cc_start: 0.9145 (ptp90) cc_final: 0.8909 (tpp-160) REVERT: B 27 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 31 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8149 (mm-30) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 0.0835 time to fit residues: 11.5092 Evaluate side-chains 94 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 39 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.105247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077154 restraints weight = 26030.855| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 5.13 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7313 Z= 0.115 Angle : 0.649 12.356 9920 Z= 0.303 Chirality : 0.041 0.174 1149 Planarity : 0.004 0.047 1297 Dihedral : 4.091 24.212 990 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.52 % Allowed : 19.55 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 917 helix: 1.17 (0.21), residues: 656 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 851 TYR 0.037 0.001 TYR A 76 PHE 0.007 0.001 PHE A 800 TRP 0.010 0.001 TRP A 430 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7313) covalent geometry : angle 0.64908 ( 9920) hydrogen bonds : bond 0.03318 ( 419) hydrogen bonds : angle 4.07609 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.7839 (mmm) cc_final: 0.7528 (mmm) REVERT: A 181 MET cc_start: 0.5909 (tpt) cc_final: 0.5325 (tpt) REVERT: A 196 ASN cc_start: 0.9392 (m-40) cc_final: 0.9023 (m110) REVERT: A 250 GLN cc_start: 0.8705 (pm20) cc_final: 0.8151 (pm20) REVERT: A 296 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8206 (tm-30) REVERT: A 319 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (mm) REVERT: A 355 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9180 (mp) REVERT: A 627 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8694 (p0) REVERT: A 661 TYR cc_start: 0.8546 (p90) cc_final: 0.8216 (p90) REVERT: A 766 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 842 MET cc_start: 0.8398 (ttt) cc_final: 0.7959 (ttt) REVERT: A 870 ARG cc_start: 0.9122 (ptp90) cc_final: 0.8871 (tpp-160) REVERT: B 27 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 31 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8125 (mm-30) outliers start: 20 outliers final: 10 residues processed: 102 average time/residue: 0.0782 time to fit residues: 11.3203 Evaluate side-chains 93 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.104890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.076838 restraints weight = 26058.992| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 5.12 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7313 Z= 0.112 Angle : 0.666 15.788 9920 Z= 0.308 Chirality : 0.041 0.171 1149 Planarity : 0.003 0.043 1297 Dihedral : 3.999 24.404 990 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.77 % Allowed : 19.80 % Favored : 77.43 % 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 are not related in a simple way. whole: 1.20 (0.29), residues: 917 helix: 1.17 (0.21), residues: 659 sheet: None (None), residues: 0 loop : 0.04 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 613 TYR 0.037 0.001 TYR A 76 PHE 0.006 0.001 PHE A 800 TRP 0.009 0.001 TRP A 126 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7313) covalent geometry : angle 0.66642 ( 9920) hydrogen bonds : bond 0.03308 ( 419) hydrogen bonds : angle 4.10461 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5804 (tpt) cc_final: 0.5258 (tpt) REVERT: A 196 ASN cc_start: 0.9395 (m-40) cc_final: 0.9024 (m110) REVERT: A 296 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8208 (tm-30) REVERT: A 319 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 627 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8736 (p0) REVERT: A 661 TYR cc_start: 0.8543 (p90) cc_final: 0.8217 (p90) REVERT: A 766 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 870 ARG cc_start: 0.9121 (ptp90) cc_final: 0.8856 (tpp-160) REVERT: B 27 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 31 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8163 (mm-30) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 0.0806 time to fit residues: 11.4636 Evaluate side-chains 89 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.100337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072662 restraints weight = 25807.264| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.88 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7313 Z= 0.237 Angle : 0.782 13.467 9920 Z= 0.377 Chirality : 0.045 0.206 1149 Planarity : 0.004 0.047 1297 Dihedral : 4.374 22.014 990 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.65 % Allowed : 20.55 % Favored : 76.80 % 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 are not related in a simple way. whole: 0.69 (0.28), residues: 917 helix: 0.82 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 852 TYR 0.035 0.002 TYR A 76 PHE 0.012 0.002 PHE A 474 TRP 0.014 0.002 TRP A 380 HIS 0.002 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 7313) covalent geometry : angle 0.78173 ( 9920) hydrogen bonds : bond 0.04401 ( 419) hydrogen bonds : angle 4.65498 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.7862 (mmm) cc_final: 0.7518 (mmm) REVERT: A 181 MET cc_start: 0.5704 (tpt) cc_final: 0.5217 (tpt) REVERT: A 196 ASN cc_start: 0.9398 (m-40) cc_final: 0.9018 (m110) REVERT: A 296 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8162 (tm-30) REVERT: A 319 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 627 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8886 (p0) REVERT: A 661 TYR cc_start: 0.8700 (p90) cc_final: 0.8385 (p90) REVERT: A 766 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 767 GLU cc_start: 0.8800 (tp30) cc_final: 0.8596 (tp30) REVERT: A 788 MET cc_start: 0.8482 (mmt) cc_final: 0.8257 (mmt) REVERT: A 845 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: A 870 ARG cc_start: 0.9153 (ptp90) cc_final: 0.8863 (tpp-160) REVERT: B 1 MET cc_start: -0.0095 (tpp) cc_final: -0.0471 (tpp) REVERT: B 27 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 31 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8263 (mm-30) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.0758 time to fit residues: 10.6207 Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.103767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.075692 restraints weight = 25800.950| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 5.03 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7313 Z= 0.125 Angle : 0.741 14.617 9920 Z= 0.345 Chirality : 0.043 0.222 1149 Planarity : 0.003 0.044 1297 Dihedral : 4.195 23.691 990 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.27 % Allowed : 20.81 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 917 helix: 1.13 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -0.20 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 852 TYR 0.037 0.002 TYR A 76 PHE 0.021 0.001 PHE A 217 TRP 0.006 0.001 TRP A 430 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7313) covalent geometry : angle 0.74061 ( 9920) hydrogen bonds : bond 0.03644 ( 419) hydrogen bonds : angle 4.34057 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.7801 (mmm) cc_final: 0.7537 (mmm) REVERT: A 181 MET cc_start: 0.5835 (tpt) cc_final: 0.5334 (tpt) REVERT: A 196 ASN cc_start: 0.9405 (m-40) cc_final: 0.9039 (m110) REVERT: A 209 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 296 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8185 (tm-30) REVERT: A 319 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 627 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8806 (p0) REVERT: A 661 TYR cc_start: 0.8593 (p90) cc_final: 0.8286 (p90) REVERT: A 766 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8606 (tt) REVERT: A 842 MET cc_start: 0.8172 (ttt) cc_final: 0.7475 (mpp) REVERT: B 1 MET cc_start: -0.0497 (tpp) cc_final: -0.0876 (tpp) REVERT: B 27 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 31 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8238 (mm-30) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.0743 time to fit residues: 10.1007 Evaluate side-chains 91 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.102453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.074089 restraints weight = 26179.401| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.07 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7313 Z= 0.157 Angle : 0.759 13.435 9920 Z= 0.359 Chirality : 0.044 0.209 1149 Planarity : 0.004 0.044 1297 Dihedral : 4.179 23.503 990 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.27 % Allowed : 20.81 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 917 helix: 1.07 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 870 TYR 0.039 0.002 TYR A 76 PHE 0.009 0.001 PHE A 261 TRP 0.009 0.001 TRP A 380 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7313) covalent geometry : angle 0.75937 ( 9920) hydrogen bonds : bond 0.03785 ( 419) hydrogen bonds : angle 4.47879 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1623.47 seconds wall clock time: 28 minutes 43.36 seconds (1723.36 seconds total)