Starting phenix.real_space_refine on Fri Oct 23 17:07:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881.map" model { file = "/net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wd1_65881/10_2026/9wd1_65881_neut.cif" } resolution = 3.31 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= 0.007 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 51 5.16 5 C 6546 2.51 5 N 1760 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7566 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 908} Chain breaks: 2 Chain: "B" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2101 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 17, 'TRANS': 244} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.19 Number of scatterers: 10292 At special positions: 0 Unit cell: (95.904, 98.496, 131.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 1 15.00 O 1934 8.00 N 1760 7.00 C 6546 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: 0.85 Conformation dependent library (CDL) restraints added in 375.3 milliseconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 47.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.675A pdb=" N LEU A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 113 " --> pdb=" O TRP A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 113' Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.931A pdb=" N ILE A 123 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 Proline residue: A 133 - end of helix removed outlier: 3.794A pdb=" N GLU A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.820A pdb=" N GLY A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.785A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.677A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.560A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.556A pdb=" N VAL A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.853A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.488A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASP A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.809A pdb=" N ASN A 512 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.518A pdb=" N GLU A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 558 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 577 through 592 removed outlier: 3.573A pdb=" N ARG A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.546A pdb=" N LYS A 635 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 removed outlier: 4.196A pdb=" N GLN A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 671 through 680 removed outlier: 4.057A pdb=" N LEU A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 697 removed outlier: 3.566A pdb=" N LEU A 688 " --> pdb=" O PRO A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 729 removed outlier: 4.634A pdb=" N ASN A 721 " --> pdb=" O GLN A 717 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.817A pdb=" N LEU A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 857 through 870 Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.726A pdb=" N SER A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 915 removed outlier: 3.605A pdb=" N LYS A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 1003 through 1013 removed outlier: 3.884A pdb=" N ASP A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 939 through 944 removed outlier: 3.818A pdb=" N LYS B 942 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS B 943 " --> pdb=" O SER B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 969 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1041 through 1045 Processing helix chain 'B' and resid 1060 through 1072 Processing helix chain 'B' and resid 1084 through 1088 removed outlier: 3.832A pdb=" N ARG B1088 " --> pdb=" O ASP B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1123 through 1140 removed outlier: 4.218A pdb=" N ARG B1128 " --> pdb=" O GLU B1124 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP B1136 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1151 removed outlier: 4.076A pdb=" N LEU B1146 " --> pdb=" O ILE B1142 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B1147 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1283 removed outlier: 3.773A pdb=" N LYS B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B1283 " --> pdb=" O ALA B1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 4.500A pdb=" N PHE A 247 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.480A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 598 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.680A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A1035 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN A 992 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A1037 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 990 " --> pdb=" O GLU A1037 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS A1039 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A 988 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 999 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 990 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.680A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.882A pdb=" N SER B 930 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 977 " --> pdb=" O SER B 930 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 16 removed outlier: 4.280A pdb=" N SER C 65 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1374 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: 1.88 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3417 1.34 - 1.46: 2272 1.46 - 1.58: 4753 1.58 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 10522 Sorted by residual: bond pdb=" N ARG A 586 " pdb=" CA ARG A 586 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.05e+00 bond pdb=" N TYR A 583 " pdb=" CA TYR A 583 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.90e+00 bond pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.59e+00 bond pdb=" N MET A 584 " pdb=" CA MET A 584 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.23e+00 bond pdb=" CB GLU C 34 " pdb=" CG GLU C 34 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 ... (remaining 10517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 13993 2.15 - 4.31: 222 4.31 - 6.46: 46 6.46 - 8.62: 3 8.62 - 10.77: 3 Bond angle restraints: 14267 Sorted by residual: angle pdb=" N CYS A 278 " pdb=" CA CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" CB MET A 489 " pdb=" CG MET A 489 " pdb=" SD MET A 489 " ideal model delta sigma weight residual 112.70 122.61 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA MET A 766 " pdb=" CB MET A 766 " pdb=" CG MET A 766 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.82e+00 angle pdb=" CA LEU A 868 " pdb=" CB LEU A 868 " pdb=" CG LEU A 868 " ideal model delta sigma weight residual 116.30 127.07 -10.77 3.50e+00 8.16e-02 9.47e+00 angle pdb=" N ARG A 586 " pdb=" CA ARG A 586 " pdb=" C ARG A 586 " ideal model delta sigma weight residual 111.82 108.29 3.53 1.16e+00 7.43e-01 9.28e+00 ... (remaining 14262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5740 17.39 - 34.79: 462 34.79 - 52.18: 100 52.18 - 69.57: 23 69.57 - 86.96: 12 Dihedral angle restraints: 6337 sinusoidal: 2583 harmonic: 3754 Sorted by residual: dihedral pdb=" CA GLY A 245 " pdb=" C GLY A 245 " pdb=" N ASP A 246 " pdb=" CA ASP A 246 " ideal model delta harmonic sigma weight residual -180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER A 284 " pdb=" C SER A 284 " pdb=" N ASP A 285 " pdb=" CA ASP A 285 " ideal model delta harmonic sigma weight residual 180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA MET A 505 " pdb=" C MET A 505 " pdb=" N ASP A 506 " pdb=" CA ASP A 506 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1121 0.040 - 0.080: 322 0.080 - 0.119: 114 0.119 - 0.159: 16 0.159 - 0.199: 2 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA TYR A 718 " pdb=" N TYR A 718 " pdb=" C TYR A 718 " pdb=" CB TYR A 718 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CB ILE B1011 " pdb=" CA ILE B1011 " pdb=" CG1 ILE B1011 " pdb=" CG2 ILE B1011 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA HIS A 712 " pdb=" N HIS A 712 " pdb=" C HIS A 712 " pdb=" CB HIS A 712 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 1572 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 772 " -0.014 2.00e-02 2.50e+03 1.68e-02 4.91e+00 pdb=" CG PHE A 772 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 772 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 772 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 772 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 772 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 772 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 712 " -0.013 2.00e-02 2.50e+03 1.55e-02 3.60e+00 pdb=" CG HIS A 712 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 712 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS A 712 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS A 712 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 712 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 653 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLU A 653 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 653 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 654 " -0.010 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3737 2.89 - 3.39: 10335 3.39 - 3.89: 17014 3.89 - 4.40: 19776 4.40 - 4.90: 32600 Nonbonded interactions: 83462 Sorted by model distance: nonbonded pdb=" OD2 ASP A1047 " pdb=" NH2 ARG B 959 " model vdw 2.383 3.120 nonbonded pdb=" O TYR C 59 " pdb=" OD1 ASN C 60 " model vdw 2.466 3.040 nonbonded pdb=" O VAL A 524 " pdb=" OG1 THR A 525 " model vdw 2.579 3.040 nonbonded pdb=" C TRP A 709 " pdb=" CG TRP A 709 " model vdw 2.584 2.792 nonbonded pdb=" N GLN A 950 " pdb=" OE1 GLN A 950 " model vdw 2.587 3.120 ... (remaining 83457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.003 0.036 10522 Z= 0.145 Angle : 0.686 10.773 14267 Z= 0.353 Chirality : 0.043 0.199 1575 Planarity : 0.005 0.042 1868 Dihedral : 14.138 86.963 3913 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.53 % Allowed : 10.24 % Favored : 89.23 % 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: -0.19 (0.23), residues: 1286 helix: 0.55 (0.22), residues: 532 sheet: 0.16 (0.40), residues: 169 loop : -0.77 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 880 TYR 0.013 0.001 TYR A 718 PHE 0.038 0.002 PHE A 772 TRP 0.026 0.002 TRP A 423 HIS 0.019 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (10522) covalent geometry : angle 0.68629 / 0.35 (14267) hydrogen bonds : bond 0.12456 / 8.31 ( 495) hydrogen bonds : angle 6.77576 / 4.71 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.8116 (mtp) cc_final: 0.7736 (ptp) REVERT: A 555 ASP cc_start: 0.8545 (t70) cc_final: 0.8324 (t0) REVERT: A 859 MET cc_start: 0.9434 (mmt) cc_final: 0.8636 (pmm) REVERT: B 981 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6740 (mmp-170) REVERT: B 1069 GLN cc_start: 0.3077 (mp10) cc_final: 0.2703 (mm-40) REVERT: B 1125 GLN cc_start: 0.7495 (tt0) cc_final: 0.7266 (pt0) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.1115 time to fit residues: 13.6014 Evaluate side-chains 81 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [98, 107, 10, 66, 124, 103, 77, 122, 91, 55, 35] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0050 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.153363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098421 restraints weight = 22168.278| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 5.07 r_work: 0.3104 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10522 Z= 0.197 Angle : 0.614 8.557 14267 Z= 0.309 Chirality : 0.042 0.173 1575 Planarity : 0.004 0.045 1868 Dihedral : 5.486 57.399 1413 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.78 % Allowed : 9.08 % Favored : 89.14 % 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: -0.01 (0.23), residues: 1286 helix: 0.76 (0.22), residues: 539 sheet: -0.06 (0.37), residues: 207 loop : -0.68 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 54 TYR 0.012 0.001 TYR A 471 PHE 0.017 0.002 PHE A 772 TRP 0.015 0.001 TRP A 423 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (10522) covalent geometry : angle 0.61450 / 0.31 (14267) hydrogen bonds : bond 0.04479 / 3.04 ( 495) hydrogen bonds : angle 5.35235 / 3.73 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.8406 (mtp) cc_final: 0.8011 (ptp) REVERT: A 555 ASP cc_start: 0.8773 (t70) cc_final: 0.8567 (t0) REVERT: A 656 PHE cc_start: 0.8744 (m-10) cc_final: 0.8460 (m-10) REVERT: A 859 MET cc_start: 0.9393 (mmt) cc_final: 0.8511 (pmm) REVERT: B 981 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7004 (mmp-170) REVERT: B 982 MET cc_start: -0.0662 (ttt) cc_final: -0.1106 (tpp) REVERT: B 1125 GLN cc_start: 0.7645 (tt0) cc_final: 0.7423 (pt0) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1008 time to fit residues: 15.0049 Evaluate side-chains 95 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Chi-restraints excluded: chain C residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [25, 88, 53, 48, 105, 41, 111, 4, 70, 64, 21] chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 40.0000 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.160369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100279 restraints weight = 21532.011| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.74 r_work: 0.3403 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10522 Z= 0.168 Angle : 0.576 8.308 14267 Z= 0.288 Chirality : 0.041 0.176 1575 Planarity : 0.004 0.047 1868 Dihedral : 5.352 59.121 1413 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.69 % Allowed : 10.42 % Favored : 87.89 % 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: 0.07 (0.23), residues: 1286 helix: 0.86 (0.23), residues: 533 sheet: 0.03 (0.37), residues: 188 loop : -0.67 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.013 0.001 TYR A 718 PHE 0.014 0.001 PHE A 857 TRP 0.013 0.001 TRP A 423 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (10522) covalent geometry : angle 0.57609 / 0.29 (14267) hydrogen bonds : bond 0.04138 / 2.81 ( 495) hydrogen bonds : angle 5.05213 / 3.52 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7351 (tpt) cc_final: 0.7103 (tpp) REVERT: A 643 HIS cc_start: 0.8990 (m170) cc_final: 0.8762 (m90) REVERT: A 656 PHE cc_start: 0.8644 (m-10) cc_final: 0.8408 (m-10) REVERT: A 859 MET cc_start: 0.9418 (mmt) cc_final: 0.8522 (pmm) REVERT: B 981 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7119 (mmp-170) REVERT: B 982 MET cc_start: -0.0698 (ttt) cc_final: -0.1194 (tpp) REVERT: B 1071 LEU cc_start: 0.2979 (OUTLIER) cc_final: 0.2677 (pp) REVERT: B 1125 GLN cc_start: 0.7746 (tt0) cc_final: 0.7546 (pt0) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.1012 time to fit residues: 14.8391 Evaluate side-chains 93 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [3, 85, 117, 122, 64, 46, 9, 34, 95, 17, 89] chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.161584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.102308 restraints weight = 21444.717| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.76 r_work: 0.3440 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10522 Z= 0.116 Angle : 0.537 7.295 14267 Z= 0.268 Chirality : 0.040 0.173 1575 Planarity : 0.004 0.045 1868 Dihedral : 5.164 59.867 1413 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.87 % Allowed : 10.86 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.23), residues: 1286 helix: 0.95 (0.23), residues: 541 sheet: 0.19 (0.38), residues: 186 loop : -0.74 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.010 0.001 TYR A 718 PHE 0.042 0.001 PHE A 637 TRP 0.012 0.001 TRP A 423 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10522) covalent geometry : angle 0.53713 / 0.27 (14267) hydrogen bonds : bond 0.03743 / 2.56 ( 495) hydrogen bonds : angle 4.83432 / 3.37 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8894 (mmm) cc_final: 0.8638 (mmt) REVERT: A 265 MET cc_start: 0.7272 (tpt) cc_final: 0.7048 (tpp) REVERT: A 637 PHE cc_start: 0.7410 (p90) cc_final: 0.7158 (p90) REVERT: A 656 PHE cc_start: 0.8629 (m-10) cc_final: 0.8407 (m-10) REVERT: A 859 MET cc_start: 0.9400 (mmt) cc_final: 0.8378 (pmm) REVERT: A 996 MET cc_start: 0.7906 (tmm) cc_final: 0.7284 (tmm) REVERT: B 981 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7096 (mmp-170) REVERT: B 982 MET cc_start: -0.0785 (ttt) cc_final: -0.1292 (tpp) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.0954 time to fit residues: 14.5453 Evaluate side-chains 96 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [106, 32, 50, 37, 80, 8, 111, 74, 26, 119, 100] chunk 106 optimal weight: 40.0000 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 74 optimal weight: 0.0980 chunk 26 optimal weight: 0.1980 chunk 119 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.158115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107201 restraints weight = 21715.439| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.88 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10522 Z= 0.122 Angle : 0.550 7.806 14267 Z= 0.272 Chirality : 0.040 0.171 1575 Planarity : 0.004 0.046 1868 Dihedral : 5.100 59.324 1413 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.14 % Allowed : 11.13 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1286 helix: 1.02 (0.23), residues: 542 sheet: 0.18 (0.38), residues: 188 loop : -0.76 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.007 0.001 TYR A 718 PHE 0.030 0.001 PHE A 637 TRP 0.011 0.001 TRP A 714 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10522) covalent geometry : angle 0.54992 / 0.27 (14267) hydrogen bonds : bond 0.03711 / 2.53 ( 495) hydrogen bonds : angle 4.76524 / 3.32 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8303 (mmm) cc_final: 0.7981 (mmt) REVERT: A 246 ASP cc_start: 0.7729 (p0) cc_final: 0.7403 (p0) REVERT: A 637 PHE cc_start: 0.7314 (p90) cc_final: 0.7103 (p90) REVERT: A 656 PHE cc_start: 0.8651 (m-10) cc_final: 0.8387 (m-10) REVERT: A 766 MET cc_start: 0.9084 (mpp) cc_final: 0.8827 (pmm) REVERT: A 859 MET cc_start: 0.9161 (mmt) cc_final: 0.8226 (pmm) REVERT: A 996 MET cc_start: 0.7985 (tmm) cc_final: 0.7298 (tmm) REVERT: A 1015 MET cc_start: 0.8693 (mmm) cc_final: 0.8198 (tpp) REVERT: B 981 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6841 (mmp-170) REVERT: B 982 MET cc_start: -0.0961 (ttt) cc_final: -0.1304 (tpp) REVERT: B 1071 LEU cc_start: 0.1964 (OUTLIER) cc_final: 0.1757 (pp) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.0974 time to fit residues: 15.1947 Evaluate side-chains 99 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [14, 50, 48, 51, 118, 103, 15, 81, 90, 110, 55] chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 chunk 55 optimal weight: 0.0270 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.157160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098479 restraints weight = 21692.540| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.50 r_work: 0.3295 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10522 Z= 0.141 Angle : 0.560 7.629 14267 Z= 0.276 Chirality : 0.041 0.172 1575 Planarity : 0.004 0.047 1868 Dihedral : 5.084 57.989 1413 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.96 % Allowed : 11.58 % Favored : 86.46 % 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: 0.19 (0.24), residues: 1286 helix: 1.05 (0.23), residues: 542 sheet: 0.17 (0.38), residues: 195 loop : -0.76 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 54 TYR 0.011 0.001 TYR A 718 PHE 0.021 0.001 PHE A 637 TRP 0.013 0.001 TRP A 714 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10522) covalent geometry : angle 0.55995 / 0.28 (14267) hydrogen bonds : bond 0.03712 / 2.53 ( 495) hydrogen bonds : angle 4.67951 / 3.27 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8910 (mmm) cc_final: 0.8637 (mmt) REVERT: A 246 ASP cc_start: 0.7796 (p0) cc_final: 0.7490 (p0) REVERT: A 637 PHE cc_start: 0.7537 (p90) cc_final: 0.7316 (p90) REVERT: A 859 MET cc_start: 0.9271 (mmt) cc_final: 0.8276 (pmm) REVERT: A 996 MET cc_start: 0.8095 (tmm) cc_final: 0.7401 (tmm) REVERT: A 1015 MET cc_start: 0.8566 (mmm) cc_final: 0.8118 (tpp) REVERT: B 981 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6891 (mmp-170) REVERT: B 982 MET cc_start: -0.0356 (ttt) cc_final: -0.1045 (tpp) REVERT: B 1071 LEU cc_start: 0.2485 (OUTLIER) cc_final: 0.2200 (pp) outliers start: 22 outliers final: 16 residues processed: 104 average time/residue: 0.0929 time to fit residues: 14.1638 Evaluate side-chains 98 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [84, 53, 88, 30, 34, 115, 28, 38, 63, 120, 78] chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.155269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096161 restraints weight = 22499.950| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.93 r_work: 0.3302 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10522 Z= 0.120 Angle : 0.568 11.802 14267 Z= 0.281 Chirality : 0.041 0.170 1575 Planarity : 0.004 0.046 1868 Dihedral : 5.038 57.238 1413 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.69 % Allowed : 11.93 % Favored : 86.38 % 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: 0.21 (0.24), residues: 1286 helix: 1.06 (0.23), residues: 542 sheet: 0.26 (0.38), residues: 186 loop : -0.77 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 54 TYR 0.014 0.001 TYR B1100 PHE 0.016 0.001 PHE A 637 TRP 0.014 0.001 TRP A 714 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10522) covalent geometry : angle 0.56767 / 0.28 (14267) hydrogen bonds : bond 0.03628 / 2.46 ( 495) hydrogen bonds : angle 4.68736 / 3.26 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8967 (mmm) cc_final: 0.8674 (mmp) REVERT: A 246 ASP cc_start: 0.7782 (p0) cc_final: 0.7473 (p0) REVERT: A 622 GLN cc_start: 0.7189 (mm110) cc_final: 0.6960 (mm-40) REVERT: A 637 PHE cc_start: 0.7480 (p90) cc_final: 0.7256 (p90) REVERT: A 859 MET cc_start: 0.9201 (mmt) cc_final: 0.8245 (pmm) REVERT: A 996 MET cc_start: 0.8168 (tmm) cc_final: 0.7544 (tmm) REVERT: A 1015 MET cc_start: 0.8329 (mmm) cc_final: 0.7949 (tpp) REVERT: B 981 ARG cc_start: 0.7098 (mmm-85) cc_final: 0.6705 (mmp-170) REVERT: B 982 MET cc_start: -0.0267 (ttt) cc_final: -0.0944 (tpp) REVERT: B 1071 LEU cc_start: 0.2329 (OUTLIER) cc_final: 0.2085 (pp) outliers start: 19 outliers final: 15 residues processed: 102 average time/residue: 0.0896 time to fit residues: 13.3626 Evaluate side-chains 98 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [127, 36, 5, 92, 55, 60, 105, 82, 58, 93, 116] chunk 127 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.159760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.101624 restraints weight = 21416.030| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.85 r_work: 0.3372 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10522 Z= 0.186 Angle : 0.604 10.669 14267 Z= 0.303 Chirality : 0.042 0.170 1575 Planarity : 0.004 0.049 1868 Dihedral : 5.163 55.166 1413 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.51 % Allowed : 12.91 % Favored : 85.57 % 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: 0.15 (0.24), residues: 1286 helix: 1.06 (0.23), residues: 536 sheet: -0.05 (0.37), residues: 204 loop : -0.73 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 54 TYR 0.011 0.001 TYR A 471 PHE 0.014 0.001 PHE A 857 TRP 0.014 0.001 TRP A 709 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10522) covalent geometry : angle 0.60433 / 0.30 (14267) hydrogen bonds : bond 0.03877 / 2.61 ( 495) hydrogen bonds : angle 4.79257 / 3.33 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8939 (mmm) cc_final: 0.8647 (mmp) REVERT: A 246 ASP cc_start: 0.7758 (p0) cc_final: 0.7462 (p0) REVERT: A 859 MET cc_start: 0.9122 (mmt) cc_final: 0.8191 (pmm) REVERT: B 981 ARG cc_start: 0.7047 (mmm-85) cc_final: 0.6424 (mmp-170) REVERT: B 982 MET cc_start: -0.0233 (ttt) cc_final: -0.0841 (tpp) REVERT: B 1071 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.2364 (pp) outliers start: 17 outliers final: 16 residues processed: 98 average time/residue: 0.0899 time to fit residues: 12.9171 Evaluate side-chains 89 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [105, 113, 42, 62, 8, 65, 96, 61, 126, 39, 44] chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.0670 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.161097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103543 restraints weight = 21523.845| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.99 r_work: 0.3425 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10522 Z= 0.126 Angle : 0.568 10.725 14267 Z= 0.281 Chirality : 0.041 0.170 1575 Planarity : 0.004 0.047 1868 Dihedral : 5.017 54.178 1412 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.78 % Allowed : 12.73 % Favored : 85.49 % 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: 0.20 (0.24), residues: 1286 helix: 1.06 (0.23), residues: 542 sheet: 0.15 (0.38), residues: 195 loop : -0.76 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 54 TYR 0.009 0.001 TYR A 718 PHE 0.016 0.001 PHE A 637 TRP 0.016 0.001 TRP A 714 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10522) covalent geometry : angle 0.56800 / 0.28 (14267) hydrogen bonds : bond 0.03528 / 2.38 ( 495) hydrogen bonds : angle 4.65900 / 3.24 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8939 (mmm) cc_final: 0.8660 (mmp) REVERT: A 774 GLN cc_start: 0.8574 (mm110) cc_final: 0.8350 (mm-40) REVERT: A 859 MET cc_start: 0.9144 (mmt) cc_final: 0.8140 (pmm) REVERT: A 996 MET cc_start: 0.8105 (tmm) cc_final: 0.7457 (tmm) REVERT: B 981 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6637 (mmp-170) REVERT: B 982 MET cc_start: -0.0370 (ttt) cc_final: -0.1001 (tpp) REVERT: B 1071 LEU cc_start: 0.2426 (OUTLIER) cc_final: 0.2164 (pp) outliers start: 20 outliers final: 14 residues processed: 91 average time/residue: 0.0954 time to fit residues: 12.7852 Evaluate side-chains 96 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [31, 2, 93, 98, 38, 122, 88, 78, 106, 43, 89] chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.160937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103690 restraints weight = 21251.128| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.91 r_work: 0.3410 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10522 Z= 0.134 Angle : 0.581 11.015 14267 Z= 0.285 Chirality : 0.041 0.169 1575 Planarity : 0.004 0.047 1868 Dihedral : 4.994 53.478 1412 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 12.91 % Favored : 85.57 % 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: 0.20 (0.24), residues: 1286 helix: 1.08 (0.23), residues: 542 sheet: 0.20 (0.38), residues: 195 loop : -0.79 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 54 TYR 0.009 0.001 TYR A 718 PHE 0.013 0.001 PHE A 857 TRP 0.012 0.001 TRP A 709 HIS 0.002 0.000 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10522) covalent geometry : angle 0.58085 / 0.29 (14267) hydrogen bonds : bond 0.03572 / 2.41 ( 495) hydrogen bonds : angle 4.61525 / 3.21 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8997 (mmm) cc_final: 0.8693 (mmp) REVERT: A 859 MET cc_start: 0.9106 (mmt) cc_final: 0.8111 (pmm) REVERT: A 996 MET cc_start: 0.8146 (tmm) cc_final: 0.7451 (tmm) REVERT: B 981 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6531 (mmp-170) REVERT: B 982 MET cc_start: -0.0318 (ttt) cc_final: -0.0984 (tpp) REVERT: B 1071 LEU cc_start: 0.2228 (OUTLIER) cc_final: 0.1993 (pp) outliers start: 17 outliers final: 15 residues processed: 99 average time/residue: 0.0952 time to fit residues: 13.9609 Evaluate side-chains 95 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 1069 GLN Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1259 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: [59, 88, 49, 108, 1, 68, 121, 89, 33, 14, 15] chunk 59 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 89 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104417 restraints weight = 21603.094| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.92 r_work: 0.3410 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10522 Z= 0.119 Angle : 0.583 11.022 14267 Z= 0.286 Chirality : 0.041 0.169 1575 Planarity : 0.004 0.046 1868 Dihedral : 4.952 52.794 1412 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.87 % Allowed : 12.82 % Favored : 85.31 % 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: 0.21 (0.23), residues: 1286 helix: 1.07 (0.23), residues: 542 sheet: 0.29 (0.38), residues: 186 loop : -0.79 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 54 TYR 0.016 0.001 TYR A 718 PHE 0.017 0.001 PHE A 772 TRP 0.014 0.001 TRP A 714 HIS 0.007 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10522) covalent geometry : angle 0.58279 / 0.29 (14267) hydrogen bonds : bond 0.03538 / 2.40 ( 495) hydrogen bonds : angle 4.64044 / 3.23 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.40 seconds wall clock time: 56 minutes 59.57 seconds (3419.57 seconds total)