Starting phenix.real_space_refine on Thu Jul 2 05:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwr_35777/07_2026/8iwr_35777_trim.cif" } resolution = 3.52 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= 0.019 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 4371 2.51 5 N 1149 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6871 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6838 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 35, 'TRANS': 857} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 1.33, per 1000 atoms: 0.19 Number of scatterers: 6871 At special positions: 0 Unit cell: (115.08, 100.8, 107.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 52 16.00 P 3 15.00 Mg 1 11.99 O 1294 8.00 N 1149 7.00 C 4371 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: 0.57 Conformation dependent library (CDL) restraints added in 370.4 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.675A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 100 through 131 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.758A pdb=" N ASN A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 256 through 287 Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.501A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 removed outlier: 3.749A pdb=" N LYS A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 4.018A pdb=" N VAL A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.626A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 removed outlier: 4.221A pdb=" N VAL A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 removed outlier: 4.021A pdb=" N SER A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.545A pdb=" N MET A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 4.218A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 683 through 723 removed outlier: 3.530A pdb=" N SER A 687 " --> pdb=" O GLN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 825 removed outlier: 3.806A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 860 removed outlier: 3.538A pdb=" N CYS A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 886 removed outlier: 3.662A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 909 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143 removed outlier: 3.747A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.481A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.481A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.601A pdb=" N GLN A 592 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 4.470A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 361 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 14.625A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 447 through 452 removed outlier: 6.888A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 465 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 476 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1149 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: 1.27 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1395 1.33 - 1.45: 1425 1.45 - 1.57: 4070 1.57 - 1.69: 5 1.69 - 1.81: 86 Bond restraints: 6981 Sorted by residual: bond pdb=" O3A ACP A1003 " pdb=" PB ACP A1003 " ideal model delta sigma weight residual 1.698 1.578 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C3B ACP A1003 " pdb=" PG ACP A1003 " ideal model delta sigma weight residual 1.875 1.785 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA THR A 352 " pdb=" C THR A 352 " ideal model delta sigma weight residual 1.526 1.470 0.057 1.35e-02 5.49e+03 1.76e+01 bond pdb=" O5' ACP A1003 " pdb=" PA ACP A1003 " ideal model delta sigma weight residual 1.659 1.581 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O1G ACP A1003 " pdb=" PG ACP A1003 " ideal model delta sigma weight residual 1.533 1.459 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 6976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 9340 2.61 - 5.23: 96 5.23 - 7.84: 12 7.84 - 10.46: 9 10.46 - 13.07: 3 Bond angle restraints: 9460 Sorted by residual: angle pdb=" N PRO A 201 " pdb=" CD PRO A 201 " pdb=" CG PRO A 201 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO A 201 " pdb=" CB PRO A 201 " pdb=" CG PRO A 201 " ideal model delta sigma weight residual 104.50 94.66 9.84 1.90e+00 2.77e-01 2.68e+01 angle pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" CD PRO A 201 " ideal model delta sigma weight residual 112.00 105.98 6.02 1.40e+00 5.10e-01 1.85e+01 angle pdb=" CB PRO A 201 " pdb=" CG PRO A 201 " pdb=" CD PRO A 201 " ideal model delta sigma weight residual 106.10 93.03 13.07 3.20e+00 9.77e-02 1.67e+01 angle pdb=" O1B ACP A1003 " pdb=" PB ACP A1003 " pdb=" O2B ACP A1003 " ideal model delta sigma weight residual 119.60 108.46 11.14 3.00e+00 1.11e-01 1.38e+01 ... (remaining 9455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.74: 3654 19.74 - 39.49: 508 39.49 - 59.23: 98 59.23 - 78.98: 11 78.98 - 98.72: 8 Dihedral angle restraints: 4279 sinusoidal: 1707 harmonic: 2572 Sorted by residual: dihedral pdb=" O1A ACP A1003 " pdb=" O3A ACP A1003 " pdb=" PA ACP A1003 " pdb=" PB ACP A1003 " ideal model delta sinusoidal sigma weight residual -48.75 49.97 -98.72 1 3.00e+01 1.11e-03 1.23e+01 dihedral pdb=" CA GLU A 129 " pdb=" C GLU A 129 " pdb=" N GLU A 130 " pdb=" CA GLU A 130 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN A 822 " pdb=" CB ASN A 822 " pdb=" CG ASN A 822 " pdb=" OD1 ASN A 822 " ideal model delta sinusoidal sigma weight residual -90.00 -159.44 69.44 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 4276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 843 0.040 - 0.079: 206 0.079 - 0.119: 78 0.119 - 0.158: 5 0.158 - 0.198: 3 Chirality restraints: 1135 Sorted by residual: chirality pdb=" C2' ACP A1003 " pdb=" C1' ACP A1003 " pdb=" C3' ACP A1003 " pdb=" O2' ACP A1003 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CB ILE A 894 " pdb=" CA ILE A 894 " pdb=" CG1 ILE A 894 " pdb=" CG2 ILE A 894 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA THR A 354 " pdb=" N THR A 354 " pdb=" C THR A 354 " pdb=" CB THR A 354 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1132 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 137 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 72 " 0.012 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP A 72 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 72 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 72 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 72 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 72 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 861 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 862 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " -0.027 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 188 2.70 - 3.25: 6741 3.25 - 3.80: 10892 3.80 - 4.35: 13106 4.35 - 4.90: 22292 Nonbonded interactions: 53219 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O1G ACP A1003 " model vdw 2.149 2.170 nonbonded pdb=" OD1 ASN A 701 " pdb=" NE2 GLN A 829 " model vdw 2.206 3.120 nonbonded pdb=" O ILE A 836 " pdb=" OG SER A 840 " model vdw 2.263 3.040 nonbonded pdb=" NE2 GLN A 865 " pdb=" O GLU A 871 " model vdw 2.285 3.120 nonbonded pdb=" O PRO A 744 " pdb=" OG SER A 748 " model vdw 2.293 3.040 ... (remaining 53214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 6981 Z= 0.222 Angle : 0.701 13.074 9460 Z= 0.343 Chirality : 0.040 0.198 1135 Planarity : 0.004 0.056 1190 Dihedral : 18.077 98.719 2615 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.26 % Allowed : 30.73 % Favored : 69.01 % 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: 0.89 (0.29), residues: 891 helix: 2.07 (0.24), residues: 465 sheet: -1.15 (0.72), residues: 67 loop : -1.09 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 448 TYR 0.003 0.000 TYR A 696 PHE 0.017 0.001 PHE A 118 TRP 0.035 0.002 TRP A 72 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 ( 6981) covalent geometry : angle 0.70137 / 0.34 ( 9460) hydrogen bonds : bond 0.14213 / 9.20 ( 385) hydrogen bonds : angle 5.80848 / 4.46 ( 1149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7222 (mmmt) REVERT: A 264 LEU cc_start: 0.7846 (tt) cc_final: 0.7518 (tp) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.0740 time to fit residues: 14.2403 Evaluate side-chains 130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 149 HIS A 829 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149387 restraints weight = 9072.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152948 restraints weight = 5927.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155506 restraints weight = 4442.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157252 restraints weight = 3629.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158224 restraints weight = 3158.445| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6981 Z= 0.162 Angle : 0.602 6.852 9460 Z= 0.311 Chirality : 0.043 0.146 1135 Planarity : 0.005 0.045 1190 Dihedral : 6.953 75.281 974 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.04 % Allowed : 27.99 % Favored : 67.97 % 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: 0.76 (0.29), residues: 891 helix: 1.97 (0.24), residues: 461 sheet: -1.47 (0.59), residues: 87 loop : -1.00 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 448 TYR 0.017 0.001 TYR A 618 PHE 0.012 0.001 PHE A 821 TRP 0.014 0.001 TRP A 72 HIS 0.003 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6981) covalent geometry : angle 0.60218 / 0.31 ( 9460) hydrogen bonds : bond 0.03903 / 2.67 ( 385) hydrogen bonds : angle 4.57804 / 3.43 ( 1149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 62 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 153 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8227 (ptm160) REVERT: A 264 LEU cc_start: 0.8041 (tt) cc_final: 0.7690 (tp) REVERT: A 281 MET cc_start: 0.6608 (tpt) cc_final: 0.6408 (tpp) REVERT: A 717 ILE cc_start: 0.6368 (mm) cc_final: 0.5797 (mm) REVERT: A 794 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7228 (m-80) outliers start: 31 outliers final: 17 residues processed: 163 average time/residue: 0.0665 time to fit residues: 15.1257 Evaluate side-chains 152 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 140 HIS A 372 HIS A 419 ASN A 506 GLN A 605 GLN A 633 GLN A 822 ASN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134328 restraints weight = 9035.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136568 restraints weight = 6452.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137727 restraints weight = 5245.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138167 restraints weight = 4218.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138634 restraints weight = 3812.746| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6981 Z= 0.225 Angle : 0.702 10.305 9460 Z= 0.363 Chirality : 0.046 0.174 1135 Planarity : 0.005 0.056 1190 Dihedral : 6.683 54.751 973 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.77 % Allowed : 25.26 % Favored : 67.97 % 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: 0.22 (0.28), residues: 891 helix: 1.37 (0.24), residues: 470 sheet: -1.90 (0.55), residues: 91 loop : -0.98 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 842 TYR 0.015 0.002 TYR A 618 PHE 0.018 0.002 PHE A 821 TRP 0.010 0.001 TRP A 285 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 ( 6981) covalent geometry : angle 0.70165 / 0.36 ( 9460) hydrogen bonds : bond 0.05491 / 3.80 ( 385) hydrogen bonds : angle 4.89202 / 3.61 ( 1149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8280 (mmmt) REVERT: A 264 LEU cc_start: 0.8115 (tt) cc_final: 0.7824 (tp) REVERT: A 281 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6726 (tpp) REVERT: A 298 SER cc_start: 0.8622 (m) cc_final: 0.8318 (m) REVERT: A 748 SER cc_start: 0.9255 (m) cc_final: 0.8389 (m) REVERT: A 794 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7746 (m-80) outliers start: 52 outliers final: 31 residues processed: 179 average time/residue: 0.0787 time to fit residues: 19.0812 Evaluate side-chains 163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS ** A 869 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144095 restraints weight = 9251.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145606 restraints weight = 7221.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147095 restraints weight = 6057.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147614 restraints weight = 4882.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148014 restraints weight = 4298.480| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6981 Z= 0.164 Angle : 0.609 7.582 9460 Z= 0.314 Chirality : 0.043 0.157 1135 Planarity : 0.004 0.066 1190 Dihedral : 6.388 51.706 973 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.60 % Allowed : 26.43 % Favored : 67.97 % 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: 0.39 (0.29), residues: 891 helix: 1.63 (0.24), residues: 463 sheet: -1.98 (0.55), residues: 93 loop : -0.99 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.009 0.001 TYR A 122 PHE 0.011 0.001 PHE A 176 TRP 0.013 0.001 TRP A 72 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6981) covalent geometry : angle 0.60947 / 0.31 ( 9460) hydrogen bonds : bond 0.04481 / 3.13 ( 385) hydrogen bonds : angle 4.61082 / 3.42 ( 1149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6775 (tp30) cc_final: 0.6556 (tp30) REVERT: A 93 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 264 LEU cc_start: 0.8099 (tt) cc_final: 0.7809 (tp) REVERT: A 281 MET cc_start: 0.6954 (tpt) cc_final: 0.6713 (tpp) REVERT: A 298 SER cc_start: 0.8678 (m) cc_final: 0.8433 (m) REVERT: A 485 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: A 748 SER cc_start: 0.9137 (m) cc_final: 0.8459 (m) outliers start: 43 outliers final: 30 residues processed: 171 average time/residue: 0.0725 time to fit residues: 16.7284 Evaluate side-chains 162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 22 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 ASN A 765 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.185801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152649 restraints weight = 9133.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152669 restraints weight = 7509.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154299 restraints weight = 6359.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155751 restraints weight = 4952.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156011 restraints weight = 4233.635| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.125 Angle : 0.572 8.198 9460 Z= 0.292 Chirality : 0.041 0.145 1135 Planarity : 0.004 0.075 1190 Dihedral : 6.095 48.645 973 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.21 % Allowed : 27.21 % Favored : 67.58 % 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: 0.59 (0.29), residues: 891 helix: 1.83 (0.24), residues: 465 sheet: -1.75 (0.54), residues: 103 loop : -0.98 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.010 0.001 TYR A 618 PHE 0.011 0.001 PHE A 725 TRP 0.016 0.001 TRP A 72 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6981) covalent geometry : angle 0.57177 / 0.29 ( 9460) hydrogen bonds : bond 0.03926 / 2.76 ( 385) hydrogen bonds : angle 4.40584 / 3.28 ( 1149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7634 (tt) REVERT: A 129 GLU cc_start: 0.6760 (pp20) cc_final: 0.6555 (pp20) REVERT: A 130 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6219 (mm-30) REVERT: A 227 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8325 (mmmt) REVERT: A 264 LEU cc_start: 0.8075 (tt) cc_final: 0.7808 (tp) REVERT: A 298 SER cc_start: 0.8580 (m) cc_final: 0.8330 (m) REVERT: A 381 ASN cc_start: 0.8000 (p0) cc_final: 0.7759 (p0) REVERT: A 485 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: A 536 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7682 (mt) REVERT: A 717 ILE cc_start: 0.7564 (mm) cc_final: 0.7288 (mm) REVERT: A 748 SER cc_start: 0.9069 (m) cc_final: 0.8373 (m) outliers start: 40 outliers final: 28 residues processed: 173 average time/residue: 0.0747 time to fit residues: 17.5241 Evaluate side-chains 163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150678 restraints weight = 9085.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152360 restraints weight = 6892.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152857 restraints weight = 5966.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153433 restraints weight = 5397.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154518 restraints weight = 4590.489| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.127 Angle : 0.574 6.977 9460 Z= 0.295 Chirality : 0.042 0.234 1135 Planarity : 0.004 0.074 1190 Dihedral : 5.972 47.272 973 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.38 % Allowed : 25.78 % Favored : 67.84 % 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: 0.56 (0.29), residues: 891 helix: 1.81 (0.24), residues: 466 sheet: -1.80 (0.54), residues: 103 loop : -1.00 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.017 0.001 TYR A 618 PHE 0.011 0.001 PHE A 725 TRP 0.017 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6981) covalent geometry : angle 0.57353 / 0.30 ( 9460) hydrogen bonds : bond 0.03852 / 2.71 ( 385) hydrogen bonds : angle 4.37746 / 3.26 ( 1149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 121 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 130 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7011 (mm-30) REVERT: A 148 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 227 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8342 (mmmt) REVERT: A 264 LEU cc_start: 0.8079 (tt) cc_final: 0.7825 (tp) REVERT: A 485 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: A 717 ILE cc_start: 0.7587 (mm) cc_final: 0.7331 (mm) REVERT: A 748 SER cc_start: 0.9031 (m) cc_final: 0.8382 (m) outliers start: 49 outliers final: 32 residues processed: 178 average time/residue: 0.0744 time to fit residues: 17.9557 Evaluate side-chains 169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145468 restraints weight = 9075.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148534 restraints weight = 6258.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150630 restraints weight = 4876.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151912 restraints weight = 4128.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153015 restraints weight = 3683.472| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.135 Angle : 0.581 7.232 9460 Z= 0.298 Chirality : 0.042 0.208 1135 Planarity : 0.004 0.076 1190 Dihedral : 5.933 46.272 973 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.60 % Allowed : 26.56 % Favored : 67.84 % 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: 0.55 (0.29), residues: 891 helix: 1.79 (0.24), residues: 466 sheet: -1.78 (0.54), residues: 103 loop : -0.99 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.020 0.001 TYR A 618 PHE 0.019 0.001 PHE A 274 TRP 0.020 0.001 TRP A 72 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6981) covalent geometry : angle 0.58072 / 0.30 ( 9460) hydrogen bonds : bond 0.03923 / 2.77 ( 385) hydrogen bonds : angle 4.38923 / 3.26 ( 1149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7612 (tt) REVERT: A 129 GLU cc_start: 0.6867 (pp20) cc_final: 0.6630 (pp20) REVERT: A 148 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: A 227 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8364 (mmmt) REVERT: A 264 LEU cc_start: 0.8063 (tt) cc_final: 0.7815 (tp) REVERT: A 360 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: A 485 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 641 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7171 (ttm) REVERT: A 717 ILE cc_start: 0.7678 (mm) cc_final: 0.7438 (mm) REVERT: A 748 SER cc_start: 0.9061 (m) cc_final: 0.8487 (m) outliers start: 43 outliers final: 32 residues processed: 168 average time/residue: 0.0799 time to fit residues: 17.9935 Evaluate side-chains 166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.180574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146173 restraints weight = 9137.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149328 restraints weight = 6206.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151483 restraints weight = 4791.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152890 restraints weight = 4021.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153728 restraints weight = 3569.905| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6981 Z= 0.146 Angle : 0.617 11.390 9460 Z= 0.314 Chirality : 0.042 0.191 1135 Planarity : 0.005 0.075 1190 Dihedral : 5.953 45.517 973 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.99 % Allowed : 26.43 % Favored : 67.58 % 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: 0.49 (0.29), residues: 891 helix: 1.77 (0.24), residues: 466 sheet: -1.71 (0.56), residues: 97 loop : -1.13 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.024 0.001 TYR A 618 PHE 0.013 0.001 PHE A 478 TRP 0.021 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6981) covalent geometry : angle 0.61661 / 0.31 ( 9460) hydrogen bonds : bond 0.04032 / 2.85 ( 385) hydrogen bonds : angle 4.44893 / 3.31 ( 1149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 148 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 227 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8388 (mmmt) REVERT: A 264 LEU cc_start: 0.8062 (tt) cc_final: 0.7819 (tp) REVERT: A 360 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: A 485 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: A 717 ILE cc_start: 0.7694 (mm) cc_final: 0.7465 (mm) REVERT: A 748 SER cc_start: 0.9048 (m) cc_final: 0.8538 (m) outliers start: 46 outliers final: 37 residues processed: 175 average time/residue: 0.0836 time to fit residues: 19.5797 Evaluate side-chains 171 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN A 855 GLN 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 = 0.181711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146568 restraints weight = 9115.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149738 restraints weight = 6193.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151865 restraints weight = 4801.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153158 restraints weight = 4042.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154242 restraints weight = 3611.401| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.139 Angle : 0.611 7.082 9460 Z= 0.314 Chirality : 0.042 0.194 1135 Planarity : 0.005 0.075 1190 Dihedral : 5.935 44.871 973 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.12 % Allowed : 26.30 % Favored : 67.58 % 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: 0.50 (0.29), residues: 891 helix: 1.75 (0.24), residues: 467 sheet: -1.67 (0.57), residues: 97 loop : -1.12 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.020 0.001 TYR A 618 PHE 0.026 0.002 PHE A 118 TRP 0.024 0.001 TRP A 72 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6981) covalent geometry : angle 0.61095 / 0.31 ( 9460) hydrogen bonds : bond 0.03974 / 2.80 ( 385) hydrogen bonds : angle 4.42574 / 3.29 ( 1149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 148 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 227 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8391 (mmmt) REVERT: A 264 LEU cc_start: 0.8032 (tt) cc_final: 0.7777 (tp) REVERT: A 274 PHE cc_start: 0.8491 (m-80) cc_final: 0.8035 (m-10) REVERT: A 360 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7824 (mtt) REVERT: A 485 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 641 MET cc_start: 0.7453 (ttm) cc_final: 0.7247 (ttm) REVERT: A 717 ILE cc_start: 0.7675 (mm) cc_final: 0.7405 (mm) REVERT: A 748 SER cc_start: 0.9008 (m) cc_final: 0.8581 (m) outliers start: 47 outliers final: 40 residues processed: 168 average time/residue: 0.0724 time to fit residues: 16.4741 Evaluate side-chains 173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150136 restraints weight = 9085.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150882 restraints weight = 7817.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152318 restraints weight = 6716.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152955 restraints weight = 5132.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153607 restraints weight = 4430.878| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6981 Z= 0.141 Angle : 0.620 7.471 9460 Z= 0.320 Chirality : 0.042 0.193 1135 Planarity : 0.005 0.079 1190 Dihedral : 5.913 44.410 973 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.12 % Allowed : 26.56 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.29), residues: 891 helix: 1.69 (0.24), residues: 473 sheet: -1.65 (0.57), residues: 97 loop : -1.05 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.021 0.001 TYR A 618 PHE 0.025 0.002 PHE A 118 TRP 0.025 0.001 TRP A 72 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6981) covalent geometry : angle 0.61984 / 0.32 ( 9460) hydrogen bonds : bond 0.03977 / 2.80 ( 385) hydrogen bonds : angle 4.43564 / 3.30 ( 1149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 121 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: A 148 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 227 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8391 (mmmt) REVERT: A 264 LEU cc_start: 0.8054 (tt) cc_final: 0.7802 (tp) REVERT: A 274 PHE cc_start: 0.8483 (m-80) cc_final: 0.8068 (m-10) REVERT: A 485 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 748 SER cc_start: 0.9024 (m) cc_final: 0.8787 (m) outliers start: 47 outliers final: 38 residues processed: 172 average time/residue: 0.0724 time to fit residues: 16.7793 Evaluate side-chains 173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN A 765 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147239 restraints weight = 9134.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150426 restraints weight = 6158.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152453 restraints weight = 4767.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154011 restraints weight = 4009.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154856 restraints weight = 3560.852| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6981 Z= 0.134 Angle : 0.631 12.983 9460 Z= 0.318 Chirality : 0.042 0.193 1135 Planarity : 0.005 0.078 1190 Dihedral : 5.883 43.958 973 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.47 % Allowed : 27.73 % Favored : 66.80 % 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: 0.49 (0.29), residues: 891 helix: 1.72 (0.24), residues: 473 sheet: -1.71 (0.56), residues: 97 loop : -1.10 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 153 TYR 0.028 0.001 TYR A 618 PHE 0.025 0.001 PHE A 118 TRP 0.025 0.001 TRP A 72 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 6981) covalent geometry : angle 0.63063 / 0.32 ( 9460) hydrogen bonds : bond 0.03867 / 2.72 ( 385) hydrogen bonds : angle 4.39739 / 3.28 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1326.83 seconds wall clock time: 23 minutes 40.78 seconds (1420.78 seconds total)