Starting phenix.real_space_refine on Tue Jun 17 22:19:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325.map" model { file = "/net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dz6_47325/06_2025/9dz6_47325_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 P 3 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 6532 2.51 5 N 1645 2.21 5 O 1846 1.98 5 H 10125 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20204 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 17384 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 40, 'TRANS': 1015} Chain breaks: 6 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2787 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.93, per 1000 atoms: 0.49 Number of scatterers: 20204 At special positions: 0 Unit cell: (85.078, 109.858, 129.682, 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) S 52 16.00 P 3 15.00 Mg 1 11.99 O 1846 8.00 N 1645 7.00 C 6532 6.00 H 10125 1.00 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: 5.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 78.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 102 through 121 removed outlier: 3.686A pdb=" N ARG A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 153 through 172 Processing helix chain 'A' and resid 176 through 195 removed outlier: 5.768A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.548A pdb=" N VAL A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.739A pdb=" N LYS A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.670A pdb=" N TRP A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 235 Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.958A pdb=" N THR A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.816A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.820A pdb=" N SER A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.711A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.606A pdb=" N CYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 377 through 394 removed outlier: 4.153A pdb=" N THR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.832A pdb=" N LYS A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.662A pdb=" N GLN A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 4.010A pdb=" N LYS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 464 Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 498 through 525 removed outlier: 3.650A pdb=" N LYS A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 552 removed outlier: 3.624A pdb=" N LEU A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.842A pdb=" N THR A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.551A pdb=" N LYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 627 removed outlier: 3.758A pdb=" N ALA A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 removed outlier: 4.426A pdb=" N LYS A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 removed outlier: 3.737A pdb=" N SER A 640 " --> pdb=" O PRO A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 668 removed outlier: 3.594A pdb=" N SER A 656 " --> pdb=" O HIS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 686 Proline residue: A 683 - end of helix Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 733 through 751 removed outlier: 3.688A pdb=" N SER A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 769 through 785 Proline residue: A 782 - end of helix removed outlier: 3.550A pdb=" N VAL A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 802 removed outlier: 4.049A pdb=" N HIS A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 removed outlier: 4.098A pdb=" N GLY A 809 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 4.402A pdb=" N SER A 816 " --> pdb=" O THR A 812 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 878 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 887 through 898 removed outlier: 4.038A pdb=" N ILE A 898 " --> pdb=" O ASN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 929 removed outlier: 4.401A pdb=" N ARG A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 938 through 941 Processing helix chain 'A' and resid 942 through 960 removed outlier: 3.761A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1002 Processing helix chain 'A' and resid 1018 through 1029 removed outlier: 3.822A pdb=" N GLU A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A1025 " --> pdb=" O MET A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1046 Proline residue: A1036 - end of helix removed outlier: 3.617A pdb=" N SER A1046 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1068 removed outlier: 5.121A pdb=" N THR A1065 " --> pdb=" O LYS A1061 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER A1066 " --> pdb=" O CYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1081 Processing helix chain 'A' and resid 1081 through 1087 Processing helix chain 'A' and resid 1100 through 1115 removed outlier: 3.847A pdb=" N THR A1113 " --> pdb=" O VAL A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1127 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.053A pdb=" N TYR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 56 removed outlier: 7.009A pdb=" N PHE B 13 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TRP B 66 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 15 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 68 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 17 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 147 " --> pdb=" O ILE B 119 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1863 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: 7.45 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10100 1.03 - 1.23: 29 1.23 - 1.42: 4275 1.42 - 1.61: 5945 1.61 - 1.81: 79 Bond restraints: 20428 Sorted by residual: bond pdb=" C LEU A 870 " pdb=" O LEU A 870 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" C ARG A 757 " pdb=" O ARG A 757 " ideal model delta sigma weight residual 1.236 1.205 0.032 1.26e-02 6.30e+03 6.33e+00 bond pdb=" N PHE A 899 " pdb=" CA PHE A 899 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.05e+00 bond pdb=" N PHE B 159 " pdb=" CA PHE B 159 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.54e+00 bond pdb=" N LEU A 952 " pdb=" CA LEU A 952 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.15e+00 ... (remaining 20423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 35569 1.20 - 2.40: 1313 2.40 - 3.59: 74 3.59 - 4.79: 29 4.79 - 5.99: 6 Bond angle restraints: 36991 Sorted by residual: angle pdb=" CA ASN A 230 " pdb=" C ASN A 230 " pdb=" O ASN A 230 " ideal model delta sigma weight residual 120.42 116.21 4.21 1.06e+00 8.90e-01 1.58e+01 angle pdb=" N ASP A 263 " pdb=" CA ASP A 263 " pdb=" C ASP A 263 " ideal model delta sigma weight residual 111.24 106.10 5.14 1.38e+00 5.25e-01 1.39e+01 angle pdb=" CA ASP A 263 " pdb=" CB ASP A 263 " pdb=" CG ASP A 263 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA ASP B 150 " pdb=" CB ASP B 150 " pdb=" CG ASP B 150 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA ASP B 150 " pdb=" C ASP B 150 " pdb=" O ASP B 150 " ideal model delta sigma weight residual 120.46 117.10 3.36 1.07e+00 8.73e-01 9.89e+00 ... (remaining 36986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 9313 31.89 - 63.78: 210 63.78 - 95.67: 35 95.67 - 127.56: 1 127.56 - 159.46: 2 Dihedral angle restraints: 9561 sinusoidal: 5186 harmonic: 4375 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -54.86 159.46 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O5' GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PA GTP B 201 " pdb=" PB GTP B 201 " ideal model delta sinusoidal sigma weight residual 274.12 136.96 137.16 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual 291.08 175.97 115.11 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 9558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1063 0.030 - 0.061: 381 0.061 - 0.091: 97 0.091 - 0.121: 40 0.121 - 0.152: 7 Chirality restraints: 1588 Sorted by residual: chirality pdb=" CA LEU A 952 " pdb=" N LEU A 952 " pdb=" C LEU A 952 " pdb=" CB LEU A 952 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA VAL B 10 " pdb=" N VAL B 10 " pdb=" C VAL B 10 " pdb=" CB VAL B 10 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA LYS A 937 " pdb=" N LYS A 937 " pdb=" C LYS A 937 " pdb=" CB LYS A 937 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1585 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 757 " -0.589 9.50e-02 1.11e+02 5.44e-01 5.82e+03 pdb=" NE ARG A 757 " -0.126 2.00e-02 2.50e+03 pdb=" CZ ARG A 757 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 757 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 757 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG A 757 " -0.716 2.00e-02 2.50e+03 pdb="HH12 ARG A 757 " 0.804 2.00e-02 2.50e+03 pdb="HH21 ARG A 757 " 0.779 2.00e-02 2.50e+03 pdb="HH22 ARG A 757 " -0.727 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " -0.032 2.00e-02 2.50e+03 4.44e-01 2.95e+03 pdb=" CG ASN A 230 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 230 " 0.766 2.00e-02 2.50e+03 pdb="HD22 ASN A 230 " -0.770 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 159 " -0.014 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" N GLU B 160 " 0.045 2.00e-02 2.50e+03 pdb=" CA GLU B 160 " -0.011 2.00e-02 2.50e+03 pdb=" H GLU B 160 " -0.020 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 264 2.07 - 2.70: 33165 2.70 - 3.33: 61841 3.33 - 3.97: 75991 3.97 - 4.60: 122052 Nonbonded interactions: 293313 Sorted by model distance: nonbonded pdb=" O TRP A 121 " pdb="HH22 ARG A 182 " model vdw 1.433 2.450 nonbonded pdb=" OE1 GLU A 596 " pdb=" H GLU A 596 " model vdw 1.592 2.450 nonbonded pdb=" HG SER A 650 " pdb=" OE1 GLU A 653 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU A 198 " pdb=" H GLU A 198 " model vdw 1.616 2.450 nonbonded pdb=" O LYS A1025 " pdb="HD21 ASN A1029 " model vdw 1.626 2.450 ... (remaining 293308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.350 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 44.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 0.036 10303 Z= 0.188 Angle : 0.487 5.988 13963 Z= 0.275 Chirality : 0.036 0.152 1588 Planarity : 0.005 0.166 1735 Dihedral : 11.847 159.455 3831 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.60 % Rotamer: Outliers : 0.26 % Allowed : 5.38 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.25), residues: 1210 helix: 1.89 (0.18), residues: 852 sheet: 1.31 (0.88), residues: 35 loop : -0.08 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 807 HIS 0.002 0.001 HIS A 859 PHE 0.019 0.001 PHE A 570 TYR 0.010 0.001 TYR A 796 ARG 0.008 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.14673 ( 641) hydrogen bonds : angle 5.82799 ( 1863) covalent geometry : bond 0.00398 (10303) covalent geometry : angle 0.48693 (13963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8037 (mtm) cc_final: 0.7456 (ptp) REVERT: A 717 GLN cc_start: 0.9484 (tt0) cc_final: 0.9260 (tm-30) REVERT: A 896 ILE cc_start: 0.8940 (mt) cc_final: 0.8556 (tp) REVERT: A 952 LEU cc_start: 0.8114 (mt) cc_final: 0.7737 (mm) REVERT: A 1064 LEU cc_start: 0.9129 (tt) cc_final: 0.8808 (tt) REVERT: A 1083 MET cc_start: 0.8689 (mtp) cc_final: 0.8239 (mmt) REVERT: B 55 TYR cc_start: 0.8838 (m-80) cc_final: 0.8154 (m-80) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.5260 time to fit residues: 61.4412 Evaluate side-chains 58 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 300 HIS A 917 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049419 restraints weight = 78298.013| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.05 r_work: 0.2673 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10303 Z= 0.158 Angle : 0.499 5.899 13963 Z= 0.269 Chirality : 0.037 0.150 1588 Planarity : 0.004 0.048 1735 Dihedral : 8.101 158.449 1335 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.35 % Allowed : 7.14 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1210 helix: 2.06 (0.18), residues: 873 sheet: 1.45 (0.83), residues: 40 loop : 0.19 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 747 HIS 0.003 0.001 HIS B 32 PHE 0.016 0.001 PHE A 570 TYR 0.011 0.001 TYR A 796 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 641) hydrogen bonds : angle 4.54282 ( 1863) covalent geometry : bond 0.00346 (10303) covalent geometry : angle 0.49903 (13963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8128 (mtm) cc_final: 0.7605 (ptp) REVERT: A 717 GLN cc_start: 0.9475 (tt0) cc_final: 0.9258 (tm-30) REVERT: A 896 ILE cc_start: 0.9023 (mt) cc_final: 0.8621 (tp) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 0.4417 time to fit residues: 42.0150 Evaluate side-chains 55 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 876 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049975 restraints weight = 77693.146| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.08 r_work: 0.2695 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10303 Z= 0.113 Angle : 0.459 5.889 13963 Z= 0.243 Chirality : 0.036 0.137 1588 Planarity : 0.004 0.046 1735 Dihedral : 8.013 157.259 1334 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.44 % Allowed : 7.85 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1210 helix: 2.15 (0.18), residues: 873 sheet: 1.53 (0.85), residues: 40 loop : 0.20 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.001 HIS B 32 PHE 0.013 0.001 PHE A 570 TYR 0.010 0.001 TYR A 104 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 641) hydrogen bonds : angle 4.26694 ( 1863) covalent geometry : bond 0.00245 (10303) covalent geometry : angle 0.45893 (13963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8039 (mtm) cc_final: 0.7142 (ptp) REVERT: A 717 GLN cc_start: 0.9479 (tt0) cc_final: 0.9256 (tm-30) REVERT: A 896 ILE cc_start: 0.8985 (mt) cc_final: 0.8617 (tp) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.3971 time to fit residues: 40.2862 Evaluate side-chains 56 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049776 restraints weight = 78948.079| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.06 r_work: 0.2683 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10303 Z= 0.141 Angle : 0.459 5.801 13963 Z= 0.242 Chirality : 0.036 0.136 1588 Planarity : 0.004 0.043 1735 Dihedral : 7.998 157.962 1334 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.90 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 8.38 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1210 helix: 2.18 (0.18), residues: 874 sheet: 1.25 (0.83), residues: 40 loop : 0.18 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.004 0.001 HIS B 32 PHE 0.016 0.001 PHE A 570 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG A 865 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 641) hydrogen bonds : angle 4.14761 ( 1863) covalent geometry : bond 0.00316 (10303) covalent geometry : angle 0.45865 (13963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8076 (mtm) cc_final: 0.7512 (ptp) REVERT: A 717 GLN cc_start: 0.9474 (tt0) cc_final: 0.9250 (tm-30) REVERT: A 896 ILE cc_start: 0.8980 (mt) cc_final: 0.8647 (tp) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.4264 time to fit residues: 42.3781 Evaluate side-chains 57 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049436 restraints weight = 78503.583| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.10 r_work: 0.2681 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10303 Z= 0.143 Angle : 0.457 5.836 13963 Z= 0.241 Chirality : 0.036 0.136 1588 Planarity : 0.004 0.042 1735 Dihedral : 8.005 158.342 1334 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.74 % Favored : 98.18 % Rotamer: Outliers : 0.71 % Allowed : 9.17 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1210 helix: 2.25 (0.18), residues: 869 sheet: 1.15 (0.82), residues: 40 loop : 0.12 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.004 0.001 HIS B 32 PHE 0.016 0.001 PHE A 570 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 641) hydrogen bonds : angle 4.07960 ( 1863) covalent geometry : bond 0.00323 (10303) covalent geometry : angle 0.45730 (13963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8059 (mtm) cc_final: 0.7197 (ptp) REVERT: A 717 GLN cc_start: 0.9473 (tt0) cc_final: 0.9244 (tm-30) REVERT: A 896 ILE cc_start: 0.8973 (mt) cc_final: 0.8666 (tp) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.4197 time to fit residues: 41.6207 Evaluate side-chains 59 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 103 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049695 restraints weight = 78202.660| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.14 r_work: 0.2692 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10303 Z= 0.120 Angle : 0.447 5.846 13963 Z= 0.234 Chirality : 0.036 0.136 1588 Planarity : 0.004 0.043 1735 Dihedral : 7.979 157.681 1334 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.40 % Favored : 98.51 % Rotamer: Outliers : 0.79 % Allowed : 9.35 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.25), residues: 1210 helix: 2.34 (0.18), residues: 869 sheet: 1.14 (0.82), residues: 40 loop : 0.16 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.001 HIS B 32 PHE 0.013 0.001 PHE A 570 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG A 865 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 641) hydrogen bonds : angle 3.97637 ( 1863) covalent geometry : bond 0.00270 (10303) covalent geometry : angle 0.44741 (13963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLN cc_start: 0.9471 (tt0) cc_final: 0.9238 (tm-30) REVERT: A 820 TYR cc_start: 0.8758 (m-10) cc_final: 0.8549 (m-10) REVERT: A 896 ILE cc_start: 0.8947 (mt) cc_final: 0.8661 (tp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.5018 time to fit residues: 48.9398 Evaluate side-chains 59 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.049245 restraints weight = 78224.671| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.15 r_work: 0.2676 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10303 Z= 0.154 Angle : 0.459 5.808 13963 Z= 0.242 Chirality : 0.036 0.136 1588 Planarity : 0.004 0.044 1735 Dihedral : 8.002 158.452 1334 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.71 % Allowed : 9.70 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.25), residues: 1210 helix: 2.31 (0.18), residues: 871 sheet: 1.15 (0.83), residues: 40 loop : 0.18 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 807 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE A 570 TYR 0.012 0.001 TYR A 104 ARG 0.003 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 641) hydrogen bonds : angle 4.00284 ( 1863) covalent geometry : bond 0.00349 (10303) covalent geometry : angle 0.45944 (13963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLN cc_start: 0.9479 (tt0) cc_final: 0.9239 (tm-30) REVERT: A 820 TYR cc_start: 0.8766 (m-10) cc_final: 0.8550 (m-10) REVERT: A 896 ILE cc_start: 0.8920 (mt) cc_final: 0.8630 (tp) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.5957 time to fit residues: 56.9392 Evaluate side-chains 60 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 GLN A1069 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049674 restraints weight = 79533.331| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.03 r_work: 0.2708 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10303 Z= 0.168 Angle : 0.467 5.834 13963 Z= 0.246 Chirality : 0.036 0.136 1588 Planarity : 0.004 0.045 1735 Dihedral : 8.047 159.536 1334 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.93 % Rotamer: Outliers : 0.79 % Allowed : 9.88 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.25), residues: 1210 helix: 2.30 (0.18), residues: 871 sheet: 1.05 (0.82), residues: 40 loop : 0.15 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 807 HIS 0.003 0.001 HIS B 32 PHE 0.018 0.001 PHE A 570 TYR 0.012 0.001 TYR A 104 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 641) hydrogen bonds : angle 4.02209 ( 1863) covalent geometry : bond 0.00382 (10303) covalent geometry : angle 0.46650 (13963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.8872 (mtp) cc_final: 0.8429 (mtm) REVERT: A 717 GLN cc_start: 0.9440 (tt0) cc_final: 0.9223 (tm-30) REVERT: A 820 TYR cc_start: 0.8769 (m-10) cc_final: 0.8545 (m-10) REVERT: A 896 ILE cc_start: 0.8992 (mt) cc_final: 0.8706 (tp) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.4836 time to fit residues: 45.9501 Evaluate side-chains 60 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051102 restraints weight = 78774.879| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.07 r_work: 0.2745 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10303 Z= 0.095 Angle : 0.439 5.935 13963 Z= 0.227 Chirality : 0.035 0.138 1588 Planarity : 0.003 0.044 1735 Dihedral : 7.969 156.783 1334 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.49 % Favored : 98.43 % Rotamer: Outliers : 0.88 % Allowed : 10.05 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1210 helix: 2.52 (0.18), residues: 870 sheet: 0.94 (0.81), residues: 40 loop : 0.23 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 747 HIS 0.003 0.000 HIS B 32 PHE 0.012 0.001 PHE B 28 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 641) hydrogen bonds : angle 3.85086 ( 1863) covalent geometry : bond 0.00213 (10303) covalent geometry : angle 0.43866 (13963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.8806 (mtp) cc_final: 0.8377 (mtm) REVERT: A 717 GLN cc_start: 0.9445 (tt0) cc_final: 0.9221 (tm-30) REVERT: A 820 TYR cc_start: 0.8761 (m-10) cc_final: 0.8536 (m-10) REVERT: A 896 ILE cc_start: 0.8894 (mt) cc_final: 0.8653 (tp) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.4546 time to fit residues: 46.2384 Evaluate side-chains 62 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050915 restraints weight = 78873.318| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.10 r_work: 0.2741 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 10303 Z= 0.172 Angle : 0.764 59.195 13963 Z= 0.466 Chirality : 0.035 0.138 1588 Planarity : 0.003 0.044 1735 Dihedral : 7.968 156.806 1334 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.79 % Allowed : 10.23 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1210 helix: 2.52 (0.18), residues: 870 sheet: 0.93 (0.81), residues: 40 loop : 0.25 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.000 HIS B 32 PHE 0.011 0.001 PHE B 28 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 641) hydrogen bonds : angle 3.85185 ( 1863) covalent geometry : bond 0.00351 (10303) covalent geometry : angle 0.76425 (13963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.8809 (mtp) cc_final: 0.8378 (mtm) REVERT: A 717 GLN cc_start: 0.9445 (tt0) cc_final: 0.9221 (tm-30) REVERT: A 820 TYR cc_start: 0.8769 (m-10) cc_final: 0.8544 (m-10) REVERT: A 848 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: A 896 ILE cc_start: 0.8895 (mt) cc_final: 0.8652 (tp) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.4815 time to fit residues: 44.7511 Evaluate side-chains 62 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 1054 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050926 restraints weight = 79114.171| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.07 r_work: 0.2744 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 10303 Z= 0.172 Angle : 0.764 59.195 13963 Z= 0.466 Chirality : 0.035 0.138 1588 Planarity : 0.003 0.044 1735 Dihedral : 7.968 156.806 1334 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.79 % Allowed : 10.23 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1210 helix: 2.52 (0.18), residues: 870 sheet: 0.93 (0.81), residues: 40 loop : 0.25 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.003 0.000 HIS B 32 PHE 0.011 0.001 PHE B 28 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 641) hydrogen bonds : angle 3.85185 ( 1863) covalent geometry : bond 0.00351 (10303) covalent geometry : angle 0.76425 (13963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9279.12 seconds wall clock time: 159 minutes 28.07 seconds (9568.07 seconds total)