Starting phenix.real_space_refine on Fri Aug 7 12:05:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm4_52285/08_2026/9hm4_52285.map" } resolution = 3.2 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= 0.003 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 157 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 6493 2.51 5 N 1929 2.21 5 O 2581 1.98 5 H 9612 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20794 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 15760 Classifications: {'peptide': 958} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 3 Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1504 Classifications: {'RNA': 47} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 3, 'rna3p': 43} Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1085 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 17} Link IDs: {'rna2p': 4, 'rna3p': 29} Chain: "D" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 2443 Classifications: {'RNA': 76} Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 30, 'rna3p_pyr': 28} Link IDs: {'rna2p': 18, 'rna3p': 57} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.14 Number of scatterers: 20794 At special positions: 0 Unit cell: (99.19, 134.68, 129.22, 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 20 16.00 P 157 15.00 Mg 2 11.99 O 2581 8.00 N 1929 7.00 C 6493 6.00 H 9612 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: 1.74 Conformation dependent library (CDL) restraints added in 428.8 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 52.3% alpha, 14.1% beta 55 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.944A pdb=" N SER A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.533A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 removed outlier: 3.855A pdb=" N ALA A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.641A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.689A pdb=" N ILE A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.206A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.673A pdb=" N GLY A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 418 removed outlier: 3.858A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.348A pdb=" N ALA A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 516 through 530 removed outlier: 4.164A pdb=" N LYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.620A pdb=" N GLN A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.719A pdb=" N PHE A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.532A pdb=" N LEU A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 4.147A pdb=" N TRP A 613 " --> pdb=" O HIS A 609 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.503A pdb=" N LYS A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.759A pdb=" N LYS A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.604A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.790A pdb=" N LYS A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 828 through 846 removed outlier: 4.040A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 839 " --> pdb=" O TRP A 835 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 879 through 885 removed outlier: 3.511A pdb=" N LYS A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 900 removed outlier: 3.795A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 908 through 916 removed outlier: 3.805A pdb=" N LYS A 914 " --> pdb=" O VAL A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 966 Processing helix chain 'A' and resid 968 through 971 Processing helix chain 'A' and resid 972 through 977 Processing helix chain 'A' and resid 992 through 995 removed outlier: 3.685A pdb=" N LEU A 995 " --> pdb=" O GLU A 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 992 through 995' Processing helix chain 'A' and resid 996 through 1024 removed outlier: 3.738A pdb=" N ALA A1003 " --> pdb=" O ASN A 999 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A1004 " --> pdb=" O THR A1000 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A1022 " --> pdb=" O HIS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1046 Processing helix chain 'A' and resid 1050 through 1063 removed outlier: 3.689A pdb=" N LEU A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A1061 " --> pdb=" O LYS A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1079 removed outlier: 4.010A pdb=" N VAL A1077 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A1079 " --> pdb=" O MET A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1106 removed outlier: 3.875A pdb=" N GLN A1105 " --> pdb=" O GLY A1102 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A1106 " --> pdb=" O THR A1103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1102 through 1106' Processing helix chain 'A' and resid 1135 through 1137 No H-bonds generated for 'chain 'A' and resid 1135 through 1137' Processing helix chain 'A' and resid 1138 through 1158 removed outlier: 4.162A pdb=" N ASP A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 removed outlier: 3.918A pdb=" N TYR A 423 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 425 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR A 638 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 212 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU A 633 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 669 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 463 removed outlier: 5.204A pdb=" N HIS A 434 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 593 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 590 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR A 664 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.450A pdb=" N THR A 275 " --> pdb=" O VAL A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.566A pdb=" N GLU A 468 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 811 removed outlier: 3.599A pdb=" N GLY A 710 " --> pdb=" O GLY A 722 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A1030 " --> pdb=" O PHE A 709 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU A1032 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASN A 713 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY A1096 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A1029 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A1098 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS A1031 " --> pdb=" O ILE A1098 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 807 removed outlier: 4.481A pdb=" N ILE A 822 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 857 through 861 removed outlier: 6.702A pdb=" N LEU A 934 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 952 " --> pdb=" O CYS A 938 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.42 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: 9602 1.03 - 1.23: 48 1.23 - 1.42: 5275 1.42 - 1.62: 6364 1.62 - 1.81: 30 Bond restraints: 21319 Sorted by residual: bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.06e+00 bond pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.95e+00 bond pdb=" N PRO A 210 " pdb=" CA PRO A 210 " ideal model delta sigma weight residual 1.479 1.451 0.028 1.71e-02 3.42e+03 2.75e+00 bond pdb=" N1 C C 19 " pdb=" C6 C C 19 " ideal model delta sigma weight residual 1.367 1.358 0.009 6.00e-03 2.78e+04 2.16e+00 bond pdb=" N9 A B 38 " pdb=" C4 A B 38 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.69e+00 ... (remaining 21314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 38382 3.07 - 6.15: 82 6.15 - 9.22: 3 9.22 - 12.29: 1 12.29 - 15.37: 1 Bond angle restraints: 38469 Sorted by residual: angle pdb=" CA PRO A 210 " pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 112.00 96.63 15.37 1.40e+00 5.10e-01 1.20e+02 angle pdb=" O5' C C 18 " pdb=" C5' C C 18 " pdb=" C4' C C 18 " ideal model delta sigma weight residual 109.40 113.91 -4.51 8.00e-01 1.56e+00 3.18e+01 angle pdb=" O5' C C 19 " pdb=" C5' C C 19 " pdb=" C4' C C 19 " ideal model delta sigma weight residual 109.40 113.86 -4.46 8.00e-01 1.56e+00 3.10e+01 angle pdb=" N1 C D 69 " pdb=" C2 C D 69 " pdb=" O2 C D 69 " ideal model delta sigma weight residual 118.90 121.98 -3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" C1' C D 71 " pdb=" N1 C D 71 " pdb=" C2 C D 71 " ideal model delta sigma weight residual 118.80 124.26 -5.46 1.10e+00 8.26e-01 2.47e+01 ... (remaining 38464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 9586 35.70 - 71.41: 548 71.41 - 107.11: 64 107.11 - 142.81: 2 142.81 - 178.52: 5 Dihedral angle restraints: 10205 sinusoidal: 6862 harmonic: 3343 Sorted by residual: dihedral pdb=" O4' C D 74 " pdb=" C1' C D 74 " pdb=" N1 C D 74 " pdb=" C2 C D 74 " ideal model delta sinusoidal sigma weight residual 200.00 37.07 162.93 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' C D 75 " pdb=" C1' C D 75 " pdb=" N1 C D 75 " pdb=" C2 C D 75 " ideal model delta sinusoidal sigma weight residual -128.00 50.52 -178.52 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C D 72 " pdb=" C1' C D 72 " pdb=" N1 C D 72 " pdb=" C2 C D 72 " ideal model delta sinusoidal sigma weight residual -128.00 39.08 -167.08 1 1.70e+01 3.46e-03 6.56e+01 ... (remaining 10202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1463 0.041 - 0.082: 262 0.082 - 0.122: 219 0.122 - 0.163: 9 0.163 - 0.204: 3 Chirality restraints: 1956 Sorted by residual: chirality pdb=" C1' C D 5 " pdb=" O4' C D 5 " pdb=" C2' C D 5 " pdb=" N1 C D 5 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A 210 " pdb=" N PRO A 210 " pdb=" C PRO A 210 " pdb=" CB PRO A 210 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" P G D 1 " pdb=" OP1 G D 1 " pdb=" OP2 G D 1 " pdb=" O5' G D 1 " both_signs ideal model delta sigma weight residual True 2.41 2.60 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 1953 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.085 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 210 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C D 5 " -0.029 2.00e-02 2.50e+03 1.38e-02 5.21e+00 pdb=" N1 C D 5 " 0.033 2.00e-02 2.50e+03 pdb=" C2 C D 5 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C D 5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C D 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C D 5 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C D 5 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C D 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 5 " 0.003 2.00e-02 2.50e+03 pdb=" H5 C D 5 " -0.003 2.00e-02 2.50e+03 pdb=" H6 C D 5 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 19 " 0.023 2.00e-02 2.50e+03 8.80e-03 2.71e+00 pdb=" N9 G D 19 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G D 19 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G D 19 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G D 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G D 19 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G D 19 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G D 19 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G D 19 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G D 19 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G D 19 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G D 19 " -0.004 2.00e-02 2.50e+03 pdb=" H8 G D 19 " -0.001 2.00e-02 2.50e+03 pdb=" H1 G D 19 " 0.003 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 927 2.18 - 2.78: 37786 2.78 - 3.39: 52728 3.39 - 3.99: 69576 3.99 - 4.60: 107687 Nonbonded interactions: 268704 Sorted by model distance: nonbonded pdb="HH22 ARG A 473 " pdb=" OP1 C C 35 " model vdw 1.574 2.450 nonbonded pdb="HO2' G D 35 " pdb=" O4' C D 36 " model vdw 1.575 2.450 nonbonded pdb=" O PRO A 774 " pdb=" H PHE A 777 " model vdw 1.607 2.450 nonbonded pdb=" HZ2 LYS A 766 " pdb=" OP2 G B 28 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU A 715 " pdb="HO2' C D 74 " model vdw 1.608 2.450 ... (remaining 268699 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: 3.400 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: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 0.112 11707 Z= 0.181 Angle : 0.688 15.367 16517 Z= 0.553 Chirality : 0.044 0.204 1956 Planarity : 0.004 0.118 1531 Dihedral : 20.253 178.517 5508 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 0.35 % Allowed : 9.94 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.27), residues: 950 helix: -1.38 (0.25), residues: 404 sheet: -1.62 (0.45), residues: 112 loop : -0.99 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 917 TYR 0.017 0.001 TYR A 979 PHE 0.008 0.001 PHE A 725 TRP 0.014 0.001 TRP A 466 HIS 0.003 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.18 (11707) covalent geometry : angle 0.68820 / 0.55 (16517) hydrogen bonds : bond 0.23903 / 15.16 ( 480) hydrogen bonds : angle 8.20404 / 5.86 ( 1195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.2483 time to fit residues: 22.6593 Evaluate side-chains 67 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 1115 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 40.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 GLN A 974 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.176381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132862 restraints weight = 45132.657| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.68 r_work: 0.3802 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11707 Z= 0.196 Angle : 0.593 5.853 16517 Z= 0.348 Chirality : 0.038 0.191 1956 Planarity : 0.004 0.054 1531 Dihedral : 21.227 178.299 3483 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.84 % Rotamer: Outliers : 0.69 % Allowed : 10.75 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.26), residues: 950 helix: -0.74 (0.25), residues: 422 sheet: -1.15 (0.46), residues: 110 loop : -1.22 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 841 TYR 0.018 0.001 TYR A 979 PHE 0.014 0.002 PHE A1014 TRP 0.008 0.001 TRP A 466 HIS 0.004 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (11707) covalent geometry : angle 0.59343 / 0.35 (16517) hydrogen bonds : bond 0.08134 / 5.15 ( 480) hydrogen bonds : angle 5.71143 / 4.08 ( 1195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.502 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 715 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6801 (mt-10) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.2293 time to fit residues: 22.2948 Evaluate side-chains 68 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1152 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.176989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.133335 restraints weight = 44948.308| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.64 r_work: 0.3813 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11707 Z= 0.153 Angle : 0.537 5.613 16517 Z= 0.315 Chirality : 0.036 0.188 1956 Planarity : 0.004 0.039 1531 Dihedral : 21.192 177.539 3483 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.16 % Allowed : 11.33 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.26), residues: 950 helix: -0.45 (0.25), residues: 426 sheet: -1.06 (0.46), residues: 109 loop : -1.26 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 917 TYR 0.017 0.001 TYR A 979 PHE 0.011 0.001 PHE A1034 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11707) covalent geometry : angle 0.53672 / 0.31 (16517) hydrogen bonds : bond 0.06874 / 4.37 ( 480) hydrogen bonds : angle 5.15472 / 3.69 ( 1195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.328 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 413 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (tttt) REVERT: A 715 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 888 ASP cc_start: 0.8015 (m-30) cc_final: 0.7524 (t0) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.2525 time to fit residues: 24.7032 Evaluate side-chains 71 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.135306 restraints weight = 45117.023| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.68 r_work: 0.3830 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11707 Z= 0.119 Angle : 0.497 7.196 16517 Z= 0.288 Chirality : 0.035 0.194 1956 Planarity : 0.003 0.039 1531 Dihedral : 21.125 176.527 3481 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 1.73 % Allowed : 10.98 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.27), residues: 950 helix: -0.13 (0.25), residues: 427 sheet: -0.94 (0.46), residues: 111 loop : -1.25 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.015 0.001 TYR A 979 PHE 0.009 0.001 PHE A1034 TRP 0.007 0.001 TRP A 424 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (11707) covalent geometry : angle 0.49723 / 0.29 (16517) hydrogen bonds : bond 0.05609 / 3.58 ( 480) hydrogen bonds : angle 4.64504 / 3.33 ( 1195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8296 (p90) cc_final: 0.7888 (p90) REVERT: A 547 ASP cc_start: 0.8667 (t70) cc_final: 0.8358 (t0) REVERT: A 601 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 715 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6781 (mt-10) outliers start: 15 outliers final: 15 residues processed: 78 average time/residue: 0.2254 time to fit residues: 23.8465 Evaluate side-chains 78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.175181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.131529 restraints weight = 45106.407| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.66 r_work: 0.3784 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11707 Z= 0.225 Angle : 0.573 7.896 16517 Z= 0.327 Chirality : 0.037 0.215 1956 Planarity : 0.004 0.086 1531 Dihedral : 21.146 175.479 3481 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 11.21 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.27), residues: 950 helix: -0.27 (0.25), residues: 429 sheet: -1.08 (0.47), residues: 109 loop : -1.49 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1114 TYR 0.018 0.002 TYR A 979 PHE 0.015 0.002 PHE A1034 TRP 0.010 0.001 TRP A 897 HIS 0.004 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (11707) covalent geometry : angle 0.57256 / 0.33 (16517) hydrogen bonds : bond 0.06439 / 4.14 ( 480) hydrogen bonds : angle 4.80523 / 3.43 ( 1195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.318 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 289 TYR cc_start: 0.8342 (p90) cc_final: 0.7908 (p90) REVERT: A 715 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6727 (mt-10) REVERT: A 888 ASP cc_start: 0.7931 (m-30) cc_final: 0.7435 (t0) REVERT: A 945 GLN cc_start: 0.8727 (mt0) cc_final: 0.8506 (mt0) outliers start: 22 outliers final: 18 residues processed: 86 average time/residue: 0.2319 time to fit residues: 27.0966 Evaluate side-chains 86 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.176109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.132561 restraints weight = 45035.301| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.67 r_work: 0.3800 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11707 Z= 0.157 Angle : 0.527 11.147 16517 Z= 0.302 Chirality : 0.036 0.199 1956 Planarity : 0.004 0.041 1531 Dihedral : 21.139 175.128 3481 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 950 helix: -0.15 (0.25), residues: 429 sheet: -1.12 (0.46), residues: 111 loop : -1.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 334 TYR 0.017 0.001 TYR A 979 PHE 0.014 0.001 PHE A1034 TRP 0.008 0.001 TRP A 897 HIS 0.003 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11707) covalent geometry : angle 0.52703 / 0.30 (16517) hydrogen bonds : bond 0.05728 / 3.67 ( 480) hydrogen bonds : angle 4.63150 / 3.31 ( 1195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8335 (p90) cc_final: 0.7899 (p90) REVERT: A 547 ASP cc_start: 0.8692 (t70) cc_final: 0.8390 (t0) REVERT: A 715 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6740 (mt-10) REVERT: A 888 ASP cc_start: 0.7931 (m-30) cc_final: 0.7422 (t0) REVERT: A 945 GLN cc_start: 0.8718 (mt0) cc_final: 0.8484 (mt0) outliers start: 19 outliers final: 19 residues processed: 84 average time/residue: 0.2339 time to fit residues: 27.1390 Evaluate side-chains 84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1064 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.175493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131746 restraints weight = 45163.740| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.70 r_work: 0.3779 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11707 Z= 0.141 Angle : 0.515 10.202 16517 Z= 0.294 Chirality : 0.036 0.194 1956 Planarity : 0.004 0.102 1531 Dihedral : 21.102 174.771 3481 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.20 % Allowed : 12.72 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.27), residues: 950 helix: -0.04 (0.26), residues: 430 sheet: -1.07 (0.47), residues: 111 loop : -1.48 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.017 0.001 TYR A1019 PHE 0.012 0.001 PHE A1034 TRP 0.007 0.001 TRP A 897 HIS 0.003 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11707) covalent geometry : angle 0.51518 / 0.29 (16517) hydrogen bonds : bond 0.05429 / 3.48 ( 480) hydrogen bonds : angle 4.51103 / 3.23 ( 1195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8334 (p90) cc_final: 0.7903 (p90) REVERT: A 414 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6569 (tm-30) REVERT: A 547 ASP cc_start: 0.8666 (t70) cc_final: 0.8353 (t0) REVERT: A 715 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6740 (mt-10) REVERT: A 888 ASP cc_start: 0.7916 (m-30) cc_final: 0.7411 (t0) REVERT: A 945 GLN cc_start: 0.8729 (mt0) cc_final: 0.8494 (mt0) outliers start: 19 outliers final: 17 residues processed: 89 average time/residue: 0.2478 time to fit residues: 29.8421 Evaluate side-chains 85 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1064 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.175237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.130878 restraints weight = 44949.381| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.73 r_work: 0.3771 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11707 Z= 0.156 Angle : 0.517 10.277 16517 Z= 0.295 Chirality : 0.036 0.195 1956 Planarity : 0.004 0.055 1531 Dihedral : 21.087 174.484 3481 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.31 % Allowed : 12.25 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.27), residues: 950 helix: 0.00 (0.26), residues: 430 sheet: -1.04 (0.47), residues: 111 loop : -1.51 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1114 TYR 0.016 0.001 TYR A 979 PHE 0.014 0.001 PHE A1034 TRP 0.008 0.001 TRP A 897 HIS 0.003 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (11707) covalent geometry : angle 0.51749 / 0.30 (16517) hydrogen bonds : bond 0.05434 / 3.50 ( 480) hydrogen bonds : angle 4.48982 / 3.22 ( 1195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8348 (p90) cc_final: 0.7907 (p90) REVERT: A 414 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6579 (tm-30) REVERT: A 547 ASP cc_start: 0.8684 (t70) cc_final: 0.8372 (t0) REVERT: A 715 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6765 (mt-10) REVERT: A 888 ASP cc_start: 0.7901 (m-30) cc_final: 0.7383 (t0) REVERT: A 945 GLN cc_start: 0.8725 (mt0) cc_final: 0.8500 (mt0) outliers start: 20 outliers final: 20 residues processed: 85 average time/residue: 0.1921 time to fit residues: 23.0705 Evaluate side-chains 87 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1064 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1157 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.176968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.133382 restraints weight = 44695.944| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.65 r_work: 0.3804 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11707 Z= 0.109 Angle : 0.481 8.955 16517 Z= 0.275 Chirality : 0.035 0.181 1956 Planarity : 0.003 0.054 1531 Dihedral : 21.042 173.951 3481 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.47 % Rotamer: Outliers : 1.97 % Allowed : 12.72 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 950 helix: 0.21 (0.26), residues: 431 sheet: -0.79 (0.49), residues: 92 loop : -1.36 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.011 0.001 TYR A 979 PHE 0.010 0.001 PHE A1034 TRP 0.009 0.001 TRP A 466 HIS 0.003 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11707) covalent geometry : angle 0.48145 / 0.27 (16517) hydrogen bonds : bond 0.04781 / 3.08 ( 480) hydrogen bonds : angle 4.27781 / 3.07 ( 1195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8319 (p90) cc_final: 0.7887 (p90) REVERT: A 414 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6620 (tm-30) REVERT: A 547 ASP cc_start: 0.8661 (t70) cc_final: 0.8344 (t0) REVERT: A 715 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 945 GLN cc_start: 0.8708 (mt0) cc_final: 0.8480 (mt0) REVERT: A 960 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.5856 (ttt-90) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.2107 time to fit residues: 24.7721 Evaluate side-chains 83 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1064 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.176910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.132821 restraints weight = 44899.983| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.71 r_work: 0.3801 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11707 Z= 0.118 Angle : 0.483 9.667 16517 Z= 0.275 Chirality : 0.034 0.182 1956 Planarity : 0.003 0.040 1531 Dihedral : 21.013 173.509 3481 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 1.85 % Allowed : 12.72 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 950 helix: 0.26 (0.26), residues: 432 sheet: -0.69 (0.49), residues: 92 loop : -1.30 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1114 TYR 0.012 0.001 TYR A 979 PHE 0.013 0.001 PHE A 511 TRP 0.007 0.001 TRP A 897 HIS 0.003 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11707) covalent geometry : angle 0.48291 / 0.28 (16517) hydrogen bonds : bond 0.04798 / 3.10 ( 480) hydrogen bonds : angle 4.23725 / 3.04 ( 1195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 TYR cc_start: 0.8335 (p90) cc_final: 0.7896 (p90) REVERT: A 414 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6648 (tm-30) REVERT: A 547 ASP cc_start: 0.8688 (t70) cc_final: 0.8374 (t0) REVERT: A 715 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 945 GLN cc_start: 0.8719 (mt0) cc_final: 0.8470 (mt0) REVERT: A 960 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5862 (ttt-90) outliers start: 16 outliers final: 15 residues processed: 80 average time/residue: 0.2222 time to fit residues: 24.8742 Evaluate side-chains 81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1034 PHE Chi-restraints excluded: chain A residue 1064 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.176034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.132334 restraints weight = 45133.813| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.75 r_work: 0.3786 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11707 Z= 0.149 Angle : 0.498 9.109 16517 Z= 0.283 Chirality : 0.035 0.189 1956 Planarity : 0.004 0.039 1531 Dihedral : 21.005 173.272 3481 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 12.60 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 950 helix: 0.25 (0.26), residues: 432 sheet: -0.74 (0.50), residues: 92 loop : -1.39 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1114 TYR 0.013 0.001 TYR A 979 PHE 0.012 0.001 PHE A1034 TRP 0.009 0.001 TRP A 897 HIS 0.003 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11707) covalent geometry : angle 0.49759 / 0.28 (16517) hydrogen bonds : bond 0.05105 / 3.30 ( 480) hydrogen bonds : angle 4.29666 / 3.08 ( 1195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.67 seconds wall clock time: 70 minutes 52.87 seconds (4252.87 seconds total)