Starting phenix.real_space_refine on Thu Feb 5 17:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm5_52286/02_2026/9hm5_52286.map" } resolution = 3.3 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= 0.004 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 85 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5809 2.51 5 N 1656 2.21 5 O 2073 1.98 5 H 8834 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18479 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 2} 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: 3.06, per 1000 atoms: 0.17 Number of scatterers: 18479 At special positions: 0 Unit cell: (99.19, 110.11, 128.31, 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 85 15.00 Mg 2 11.99 O 2073 8.00 N 1656 7.00 C 5809 6.00 H 8834 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: 1.40 Conformation dependent library (CDL) restraints added in 411.4 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: 44 helices and 9 sheets defined 50.7% alpha, 13.2% beta 32 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.630A pdb=" N GLU A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.558A pdb=" N LYS A 248 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 250 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.736A pdb=" N GLU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.559A pdb=" N GLN A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 332 through 355 removed outlier: 3.789A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.604A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.546A pdb=" N GLN A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 418 removed outlier: 3.766A pdb=" N ILE A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.272A pdb=" N ALA A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 removed outlier: 3.621A pdb=" N GLN A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.544A pdb=" N PHE A 513 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.594A 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 Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.634A pdb=" N LEU A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.939A pdb=" N TRP A 613 " --> pdb=" O HIS A 609 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 642 through 649 removed outlier: 4.097A pdb=" N LYS A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.983A pdb=" N LYS A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.521A pdb=" N ALA A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.603A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.839A pdb=" N LYS A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 827 through 846 removed outlier: 3.604A pdb=" N LEU A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 839 " --> pdb=" O TRP A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 889 through 900 removed outlier: 3.987A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 971 through 977 removed outlier: 3.796A pdb=" N LEU A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 977 " --> pdb=" O LYS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1024 removed outlier: 4.266A pdb=" N LEU A1004 " --> pdb=" O THR A1000 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A1005 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A1022 " --> pdb=" O HIS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1046 removed outlier: 3.718A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A1041 " --> pdb=" O GLY A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1064 removed outlier: 4.481A pdb=" N ASN A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1078 removed outlier: 3.861A pdb=" N VAL A1077 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1073 through 1078' Processing helix chain 'A' and resid 1128 through 1132 removed outlier: 4.386A pdb=" N ARG A1131 " --> pdb=" O ASN A1128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A1132 " --> pdb=" O SER A1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1128 through 1132' 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 1157 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 3.910A pdb=" N LEU A 428 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS A 434 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 593 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 590 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR A 664 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 669 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU A 633 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER A 671 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A 631 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 212 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR A 638 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 423 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 215 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 425 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 720 through 724 removed outlier: 7.073A pdb=" N PHE A 707 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE A1030 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 709 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLU A1032 " --> pdb=" O PHE A 709 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ILE A 711 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY A1096 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A1029 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A1098 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS A1031 " --> pdb=" O ILE A1098 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 753 Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 818 Processing sheet with id=AA8, first strand: chain 'A' and resid 857 through 861 removed outlier: 6.483A pdb=" N ALA A 936 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS A 955 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS A 938 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL A 953 " --> pdb=" O CYS A 938 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1106 through 1107 removed outlier: 3.797A pdb=" N CYS A1107 " --> pdb=" O ILE A1111 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 1.96 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: 8516 1.03 - 1.23: 347 1.23 - 1.42: 4348 1.42 - 1.61: 5582 1.61 - 1.81: 31 Bond restraints: 18824 Sorted by residual: bond pdb=" CG PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.503 1.099 0.404 3.40e-02 8.65e+02 1.41e+02 bond pdb=" C2 A B 55 " pdb=" H2 A B 55 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLU A 364 " pdb=" H GLU A 364 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLN A 361 " pdb=" H GLN A 361 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA A 356 " pdb=" H ALA A 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 33662 3.77 - 7.54: 295 7.54 - 11.32: 43 11.32 - 15.09: 3 15.09 - 18.86: 2 Bond angle restraints: 34005 Sorted by residual: angle pdb=" N PRO A 210 " pdb=" CD PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 103.20 84.34 18.86 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO A 210 " pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 112.00 95.94 16.06 1.40e+00 5.10e-01 1.32e+02 angle pdb=" CA ASN A 360 " pdb=" CB ASN A 360 " pdb=" CG ASN A 360 " ideal model delta sigma weight residual 112.60 120.19 -7.59 1.00e+00 1.00e+00 5.76e+01 angle pdb=" CA PRO A 210 " pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 104.50 90.28 14.22 1.90e+00 2.77e-01 5.60e+01 angle pdb=" N PRO A 210 " pdb=" CA PRO A 210 " pdb=" CB PRO A 210 " ideal model delta sigma weight residual 102.65 98.18 4.47 6.80e-01 2.16e+00 4.32e+01 ... (remaining 34000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 8504 35.62 - 71.24: 340 71.24 - 106.86: 35 106.86 - 142.49: 1 142.49 - 178.11: 1 Dihedral angle restraints: 8881 sinusoidal: 5538 harmonic: 3343 Sorted by residual: dihedral pdb=" C4' C D 75 " pdb=" C3' C D 75 " pdb=" C2' C D 75 " pdb=" C1' C D 75 " ideal model delta sinusoidal sigma weight residual -35.00 35.20 -70.20 1 8.00e+00 1.56e-02 9.92e+01 dihedral pdb=" C5' C D 75 " pdb=" C4' C D 75 " pdb=" C3' C D 75 " pdb=" O3' C D 75 " ideal model delta sinusoidal sigma weight residual 147.00 79.60 67.40 1 8.00e+00 1.56e-02 9.24e+01 dihedral pdb=" O4' C D 75 " pdb=" C2' C D 75 " pdb=" C1' C D 75 " pdb=" C3' C D 75 " ideal model delta sinusoidal sigma weight residual -35.00 24.13 -59.13 1 8.00e+00 1.56e-02 7.30e+01 ... (remaining 8878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1533 0.147 - 0.295: 22 0.295 - 0.442: 16 0.442 - 0.590: 20 0.590 - 0.737: 5 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CG LEU A 365 " pdb=" CB LEU A 365 " pdb=" CD1 LEU A 365 " pdb=" CD2 LEU A 365 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CG LEU A 346 " pdb=" CB LEU A 346 " pdb=" CD1 LEU A 346 " pdb=" CD2 LEU A 346 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB ILE A 353 " pdb=" CA ILE A 353 " pdb=" CG1 ILE A 353 " pdb=" CG2 ILE A 353 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1593 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 10 " 0.230 2.00e-02 2.50e+03 8.70e-02 2.46e+02 pdb=" N9 A C 10 " 0.004 2.00e-02 2.50e+03 pdb=" C8 A C 10 " -0.066 2.00e-02 2.50e+03 pdb=" N7 A C 10 " -0.033 2.00e-02 2.50e+03 pdb=" C5 A C 10 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A C 10 " 0.042 2.00e-02 2.50e+03 pdb=" N6 A C 10 " 0.123 2.00e-02 2.50e+03 pdb=" N1 A C 10 " 0.022 2.00e-02 2.50e+03 pdb=" C2 A C 10 " -0.045 2.00e-02 2.50e+03 pdb=" N3 A C 10 " -0.067 2.00e-02 2.50e+03 pdb=" C4 A C 10 " -0.038 2.00e-02 2.50e+03 pdb=" H8 A C 10 " -0.103 2.00e-02 2.50e+03 pdb=" H2 A C 10 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 59 " 0.202 2.00e-02 2.50e+03 7.75e-02 1.80e+02 pdb=" N1 U B 59 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 59 " -0.065 2.00e-02 2.50e+03 pdb=" O2 U B 59 " -0.106 2.00e-02 2.50e+03 pdb=" N3 U B 59 " -0.014 2.00e-02 2.50e+03 pdb=" C4 U B 59 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U B 59 " 0.081 2.00e-02 2.50e+03 pdb=" C5 U B 59 " -0.017 2.00e-02 2.50e+03 pdb=" C6 U B 59 " -0.041 2.00e-02 2.50e+03 pdb=" H5 U B 59 " -0.016 2.00e-02 2.50e+03 pdb=" H3 U B 59 " 0.045 2.00e-02 2.50e+03 pdb=" H6 U B 59 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 60 " 0.165 2.00e-02 2.50e+03 6.25e-02 1.37e+02 pdb=" N9 G B 60 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G B 60 " -0.065 2.00e-02 2.50e+03 pdb=" N7 G B 60 " -0.028 2.00e-02 2.50e+03 pdb=" C5 G B 60 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G B 60 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G B 60 " 0.084 2.00e-02 2.50e+03 pdb=" N1 G B 60 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 60 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G B 60 " -0.092 2.00e-02 2.50e+03 pdb=" N3 G B 60 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G B 60 " -0.013 2.00e-02 2.50e+03 pdb=" H8 G B 60 " -0.074 2.00e-02 2.50e+03 pdb=" H1 G B 60 " 0.029 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 904 2.19 - 2.79: 35301 2.79 - 3.39: 46869 3.39 - 4.00: 61569 4.00 - 4.60: 96456 Nonbonded interactions: 241099 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 600 " pdb=" O LYS A 605 " model vdw 1.584 2.450 nonbonded pdb=" HE ARG A 841 " pdb=" O LEU A 995 " model vdw 1.590 2.450 nonbonded pdb=" HZ2 LYS A 766 " pdb=" OP2 G B 28 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASN A 887 " pdb=" H ASP A 889 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASN A 316 " pdb=" H TYR A 317 " model vdw 1.619 2.450 ... (remaining 241094 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: 3.250 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.880 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.011 0.404 9990 Z= 0.514 Angle : 0.961 18.860 13839 Z= 0.575 Chirality : 0.093 0.737 1596 Planarity : 0.006 0.125 1459 Dihedral : 18.256 178.108 4350 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 0.12 % Allowed : 14.22 % Favored : 85.66 % Cbeta Deviations : 1.20 % 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: -1.28 (0.27), residues: 950 helix: -0.56 (0.26), residues: 404 sheet: -0.93 (0.44), residues: 123 loop : -0.96 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1131 TYR 0.013 0.001 TYR A 664 PHE 0.011 0.001 PHE A 957 TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.01073 ( 9990) covalent geometry : angle 0.96085 (13839) hydrogen bonds : bond 0.16939 ( 415) hydrogen bonds : angle 6.35013 ( 1083) *********************** 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 65 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.7608 (tp30) cc_final: 0.7307 (tp30) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.2376 time to fit residues: 21.2954 Evaluate side-chains 62 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.153584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128439 restraints weight = 43789.812| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.44 r_work: 0.3886 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9990 Z= 0.153 Angle : 0.566 6.147 13839 Z= 0.317 Chirality : 0.039 0.240 1596 Planarity : 0.003 0.036 1459 Dihedral : 17.108 179.342 2323 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.84 % Favored : 94.95 % Rotamer: Outliers : 1.50 % Allowed : 13.76 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.28), residues: 950 helix: -0.07 (0.26), residues: 412 sheet: -0.92 (0.43), residues: 137 loop : -0.96 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 441 TYR 0.014 0.001 TYR A 664 PHE 0.009 0.001 PHE A 591 TRP 0.009 0.001 TRP A 466 HIS 0.002 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9990) covalent geometry : angle 0.56642 (13839) hydrogen bonds : bond 0.05451 ( 415) hydrogen bonds : angle 4.69519 ( 1083) *********************** 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 85 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLU cc_start: 0.7953 (tp30) cc_final: 0.7666 (tp30) REVERT: A 417 GLU cc_start: 0.7791 (tp30) cc_final: 0.7483 (tp30) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.2240 time to fit residues: 25.5015 Evaluate side-chains 74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** 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 = 0.4194 r_free = 0.4194 target = 0.149944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.124529 restraints weight = 44081.486| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.43 r_work: 0.3744 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9990 Z= 0.235 Angle : 0.590 4.583 13839 Z= 0.327 Chirality : 0.040 0.239 1596 Planarity : 0.004 0.042 1459 Dihedral : 16.797 167.987 2321 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.21 % Favored : 93.47 % Rotamer: Outliers : 2.31 % Allowed : 15.03 % Favored : 82.66 % 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: -1.17 (0.27), residues: 950 helix: -0.24 (0.26), residues: 419 sheet: -1.01 (0.45), residues: 123 loop : -1.14 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.019 0.001 TYR A 664 PHE 0.015 0.002 PHE A 957 TRP 0.011 0.002 TRP A 466 HIS 0.004 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9990) covalent geometry : angle 0.58956 (13839) hydrogen bonds : bond 0.06031 ( 415) hydrogen bonds : angle 4.72667 ( 1083) *********************** 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 85 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6192 (mp) REVERT: A 417 GLU cc_start: 0.7953 (tp30) cc_final: 0.7749 (tp30) REVERT: A 715 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 1044 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8344 (tt0) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 0.2428 time to fit residues: 28.1885 Evaluate side-chains 72 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.158958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131746 restraints weight = 43379.927| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.39 r_work: 0.3894 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9990 Z= 0.109 Angle : 0.488 4.271 13839 Z= 0.268 Chirality : 0.036 0.200 1596 Planarity : 0.003 0.064 1459 Dihedral : 16.484 159.968 2321 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.68 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 15.95 % Favored : 82.31 % 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: -0.70 (0.28), residues: 950 helix: 0.24 (0.27), residues: 413 sheet: -0.92 (0.46), residues: 123 loop : -0.93 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1131 TYR 0.012 0.001 TYR A 664 PHE 0.008 0.001 PHE A 963 TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9990) covalent geometry : angle 0.48780 (13839) hydrogen bonds : bond 0.04287 ( 415) hydrogen bonds : angle 4.28020 ( 1083) *********************** 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 84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6051 (mp) REVERT: A 417 GLU cc_start: 0.7662 (tp30) cc_final: 0.7350 (tp30) REVERT: A 715 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 1131 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7924 (tpp80) outliers start: 15 outliers final: 11 residues processed: 83 average time/residue: 0.2585 time to fit residues: 28.9015 Evaluate side-chains 74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 ASN A1064 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127956 restraints weight = 43488.076| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.42 r_work: 0.3867 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9990 Z= 0.151 Angle : 0.502 4.303 13839 Z= 0.276 Chirality : 0.037 0.195 1596 Planarity : 0.003 0.035 1459 Dihedral : 16.427 154.863 2321 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.79 % Favored : 94.00 % Rotamer: Outliers : 2.31 % Allowed : 15.84 % Favored : 81.85 % 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: -0.78 (0.28), residues: 950 helix: 0.22 (0.27), residues: 421 sheet: -0.95 (0.44), residues: 133 loop : -1.06 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.014 0.001 TYR A 664 PHE 0.009 0.001 PHE A 591 TRP 0.009 0.001 TRP A 466 HIS 0.002 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9990) covalent geometry : angle 0.50174 (13839) hydrogen bonds : bond 0.04602 ( 415) hydrogen bonds : angle 4.28523 ( 1083) *********************** 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 78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6036 (mp) REVERT: A 417 GLU cc_start: 0.7657 (tp30) cc_final: 0.7353 (tp30) REVERT: A 715 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 1044 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8375 (tt0) outliers start: 20 outliers final: 15 residues processed: 75 average time/residue: 0.2413 time to fit residues: 24.9452 Evaluate side-chains 74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 0.0000 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.160242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133570 restraints weight = 42986.771| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.33 r_work: 0.3924 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9990 Z= 0.091 Angle : 0.457 5.227 13839 Z= 0.249 Chirality : 0.035 0.159 1596 Planarity : 0.003 0.033 1459 Dihedral : 16.328 150.863 2321 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.89 % Favored : 95.89 % Rotamer: Outliers : 1.62 % Allowed : 16.18 % Favored : 82.20 % 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: -0.43 (0.28), residues: 950 helix: 0.50 (0.27), residues: 419 sheet: -0.59 (0.46), residues: 122 loop : -0.94 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.010 0.001 TYR A 664 PHE 0.008 0.001 PHE A 963 TRP 0.007 0.001 TRP A 466 HIS 0.003 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 9990) covalent geometry : angle 0.45684 (13839) hydrogen bonds : bond 0.03670 ( 415) hydrogen bonds : angle 3.99912 ( 1083) *********************** 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 81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1044 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8387 (tt0) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.2333 time to fit residues: 25.6590 Evaluate side-chains 70 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.153246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128255 restraints weight = 43703.899| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.42 r_work: 0.3876 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9990 Z= 0.156 Angle : 0.491 4.917 13839 Z= 0.269 Chirality : 0.037 0.179 1596 Planarity : 0.003 0.033 1459 Dihedral : 16.342 150.178 2321 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.68 % Favored : 94.11 % Rotamer: Outliers : 1.73 % Allowed : 16.53 % Favored : 81.73 % 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: -0.63 (0.28), residues: 950 helix: 0.42 (0.27), residues: 420 sheet: -0.86 (0.44), residues: 135 loop : -1.07 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.014 0.001 TYR A 664 PHE 0.010 0.001 PHE A 957 TRP 0.008 0.001 TRP A 466 HIS 0.002 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9990) covalent geometry : angle 0.49109 (13839) hydrogen bonds : bond 0.04379 ( 415) hydrogen bonds : angle 4.12567 ( 1083) *********************** 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 73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1044 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8423 (tt0) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.2152 time to fit residues: 21.4580 Evaluate side-chains 69 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 ASN ** 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 = 0.4239 r_free = 0.4239 target = 0.153580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.128638 restraints weight = 43509.622| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.42 r_work: 0.3888 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9990 Z= 0.129 Angle : 0.480 5.204 13839 Z= 0.263 Chirality : 0.036 0.169 1596 Planarity : 0.003 0.034 1459 Dihedral : 16.351 148.881 2321 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 1.97 % Allowed : 16.53 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.28), residues: 950 helix: 0.46 (0.27), residues: 420 sheet: -0.84 (0.44), residues: 135 loop : -1.09 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.013 0.001 TYR A 664 PHE 0.008 0.001 PHE A 591 TRP 0.008 0.001 TRP A 466 HIS 0.002 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9990) covalent geometry : angle 0.47974 (13839) hydrogen bonds : bond 0.04154 ( 415) hydrogen bonds : angle 4.07511 ( 1083) *********************** 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 75 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5933 (mp) REVERT: A 1044 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8420 (tt0) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.2471 time to fit residues: 25.6653 Evaluate side-chains 72 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1084 ASN ** 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 = 0.4217 r_free = 0.4217 target = 0.156942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129118 restraints weight = 44655.495| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.55 r_work: 0.3854 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9990 Z= 0.179 Angle : 0.517 5.014 13839 Z= 0.284 Chirality : 0.038 0.176 1596 Planarity : 0.003 0.035 1459 Dihedral : 16.419 147.479 2321 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.32 % Favored : 93.47 % Rotamer: Outliers : 2.08 % Allowed : 16.65 % Favored : 81.27 % 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: -0.75 (0.28), residues: 950 helix: 0.36 (0.27), residues: 420 sheet: -0.94 (0.44), residues: 135 loop : -1.18 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.016 0.001 TYR A 664 PHE 0.012 0.001 PHE A 957 TRP 0.009 0.001 TRP A 466 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9990) covalent geometry : angle 0.51744 (13839) hydrogen bonds : bond 0.04785 ( 415) hydrogen bonds : angle 4.21604 ( 1083) *********************** 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 75 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5961 (mp) REVERT: A 417 GLU cc_start: 0.7708 (tp30) cc_final: 0.7340 (tp30) REVERT: A 1044 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8423 (tt0) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.2193 time to fit residues: 22.4230 Evaluate side-chains 72 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.130036 restraints weight = 44851.073| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.77 r_work: 0.3833 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9990 Z= 0.165 Angle : 0.511 5.486 13839 Z= 0.280 Chirality : 0.037 0.169 1596 Planarity : 0.003 0.034 1459 Dihedral : 16.433 146.184 2321 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.00 % Favored : 93.68 % Rotamer: Outliers : 2.08 % Allowed : 16.76 % Favored : 81.16 % 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: -0.75 (0.28), residues: 950 helix: 0.35 (0.27), residues: 420 sheet: -0.91 (0.44), residues: 133 loop : -1.18 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.015 0.001 TYR A 664 PHE 0.010 0.001 PHE A 957 TRP 0.009 0.001 TRP A 466 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9990) covalent geometry : angle 0.51106 (13839) hydrogen bonds : bond 0.04636 ( 415) hydrogen bonds : angle 4.20466 ( 1083) ********************** 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 73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5952 (mp) REVERT: A 1044 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8439 (tt0) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.2382 time to fit residues: 23.6788 Evaluate side-chains 70 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 938 CYS Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.158086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130187 restraints weight = 44778.180| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.55 r_work: 0.3868 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9990 Z= 0.140 Angle : 0.492 5.368 13839 Z= 0.270 Chirality : 0.036 0.159 1596 Planarity : 0.003 0.034 1459 Dihedral : 16.392 145.249 2321 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.11 % Favored : 93.58 % Rotamer: Outliers : 1.97 % Allowed : 16.99 % Favored : 81.04 % 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: -0.66 (0.28), residues: 950 helix: 0.43 (0.27), residues: 420 sheet: -0.89 (0.44), residues: 135 loop : -1.14 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.014 0.001 TYR A 664 PHE 0.009 0.001 PHE A 591 TRP 0.008 0.001 TRP A 466 HIS 0.002 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9990) covalent geometry : angle 0.49240 (13839) hydrogen bonds : bond 0.04300 ( 415) hydrogen bonds : angle 4.11504 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.35 seconds wall clock time: 77 minutes 16.89 seconds (4636.89 seconds total)