Starting phenix.real_space_refine on Sat Jul 4 07:00:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm5_52286/07_2026/9hm5_52286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm5_52286/07_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_52286/07_2026/9hm5_52286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm5_52286/07_2026/9hm5_52286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hm5_52286/07_2026/9hm5_52286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm5_52286/07_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-dev-6108/lib/python3.11/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: 2.96, per 1000 atoms: 0.16 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: 1.62 Conformation dependent library (CDL) restraints added in 714.4 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: 2.75 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: 4.13 Time building geometry restraints manager: 2.25 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=" C6 A B 55 " pdb=" N6 A B 55 " ideal model delta sigma weight residual 1.335 1.231 0.104 8.00e-03 1.56e+04 1.71e+02 bond pdb=" C6 A B 56 " pdb=" N6 A B 56 " ideal model delta sigma weight residual 1.335 1.232 0.103 8.00e-03 1.56e+04 1.67e+02 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=" C5 U C 17 " pdb=" C6 U C 17 " ideal model delta sigma weight residual 1.337 1.258 0.079 9.00e-03 1.23e+04 7.62e+01 bond pdb=" C5 U C 16 " pdb=" C6 U C 16 " ideal model delta sigma weight residual 1.337 1.260 0.077 9.00e-03 1.23e+04 7.41e+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=" N1 A B 55 " pdb=" C2 A B 55 " pdb=" N3 A B 55 " ideal model delta sigma weight residual 129.30 135.29 -5.99 5.00e-01 4.00e+00 1.44e+02 angle pdb=" N1 A B 56 " pdb=" C2 A B 56 " pdb=" N3 A B 56 " ideal model delta sigma weight residual 129.30 135.06 -5.76 5.00e-01 4.00e+00 1.33e+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=" N9 A B 55 " pdb=" C8 A B 55 " pdb=" N7 A B 55 " ideal model delta sigma weight residual 113.80 119.39 -5.59 5.00e-01 4.00e+00 1.25e+02 ... (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: 4.570 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: 0.080 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.560 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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= 0.630 Angle : 0.961 18.860 13839 Z= 0.790 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/Z covalent geometry : bond 0.01073 / 0.63 ( 9990) covalent geometry : angle 0.96089 / 0.79 (13839) hydrogen bonds : bond 0.16939 / 10.77 ( 415) hydrogen bonds : angle 6.35013 / 4.25 ( 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 : 0.494 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: 0.2341 time to fit residues: 21.2696 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 : 0.420 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128027 restraints weight = 43901.591| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.44 r_work: 0.3880 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9990 Z= 0.160 Angle : 0.551 5.101 13839 Z= 0.328 Chirality : 0.040 0.270 1596 Planarity : 0.004 0.045 1459 Dihedral : 17.284 179.272 2323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.16 % Allowed : 13.76 % 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: -1.01 (0.27), residues: 950 helix: -0.16 (0.26), residues: 411 sheet: -0.83 (0.45), residues: 123 loop : -1.01 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 441 TYR 0.015 0.001 TYR A 664 PHE 0.011 0.001 PHE A 228 TRP 0.008 0.001 TRP A 466 HIS 0.002 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 9990) covalent geometry : angle 0.55103 / 0.33 (13839) hydrogen bonds : bond 0.06699 / 4.43 ( 415) hydrogen bonds : angle 4.98501 / 3.37 ( 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 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLU cc_start: 0.7936 (tp30) cc_final: 0.7639 (tp30) REVERT: A 417 GLU cc_start: 0.7787 (tp30) cc_final: 0.7483 (tp30) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.1803 time to fit residues: 19.2596 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 : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.7980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.155453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.128309 restraints weight = 43663.181| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.42 r_work: 0.3854 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9990 Z= 0.204 Angle : 0.551 5.692 13839 Z= 0.326 Chirality : 0.040 0.267 1596 Planarity : 0.003 0.032 1459 Dihedral : 17.146 177.045 2321 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.89 % Favored : 93.89 % Rotamer: Outliers : 1.85 % Allowed : 15.14 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.27), residues: 950 helix: -0.14 (0.26), residues: 413 sheet: -0.97 (0.44), residues: 123 loop : -1.15 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 441 TYR 0.017 0.001 TYR A 664 PHE 0.013 0.002 PHE A 957 TRP 0.010 0.001 TRP A 466 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 9990) covalent geometry : angle 0.55066 / 0.33 (13839) hydrogen bonds : bond 0.06125 / 4.01 ( 415) hydrogen bonds : angle 4.80526 / 3.25 ( 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 82 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7032 (pp20) cc_final: 0.6563 (pp20) REVERT: A 284 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6174 (mp) REVERT: A 414 GLU cc_start: 0.7986 (tp30) cc_final: 0.7746 (tp30) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.2018 time to fit residues: 22.9313 Evaluate side-chains 75 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG 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 975 LEU 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 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: 4.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.156759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.129734 restraints weight = 43217.489| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.41 r_work: 0.3866 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9990 Z= 0.147 Angle : 0.505 5.648 13839 Z= 0.297 Chirality : 0.038 0.246 1596 Planarity : 0.003 0.035 1459 Dihedral : 16.951 172.868 2321 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 1.97 % Allowed : 15.14 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.28), residues: 950 helix: -0.04 (0.26), residues: 419 sheet: -0.94 (0.43), residues: 137 loop : -1.14 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1131 TYR 0.015 0.001 TYR A 664 PHE 0.009 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/Z covalent geometry : bond 0.00323 / 0.15 ( 9990) covalent geometry : angle 0.50494 / 0.30 (13839) hydrogen bonds : bond 0.05254 / 3.45 ( 415) hydrogen bonds : angle 4.57792 / 3.10 ( 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: 17 poor density : 67 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6143 (mp) REVERT: A 414 GLU cc_start: 0.7991 (tp30) cc_final: 0.7740 (tp30) REVERT: A 417 GLU cc_start: 0.7739 (tp30) cc_final: 0.7385 (tp30) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.2086 time to fit residues: 23.9013 Evaluate side-chains 78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 1047 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.157314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.130726 restraints weight = 43454.527| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.31 r_work: 0.3891 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9990 Z= 0.195 Angle : 0.524 4.636 13839 Z= 0.304 Chirality : 0.039 0.243 1596 Planarity : 0.004 0.086 1459 Dihedral : 16.787 170.768 2321 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.84 % Favored : 92.95 % Rotamer: Outliers : 2.54 % Allowed : 15.26 % 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: -1.14 (0.27), residues: 950 helix: -0.11 (0.26), residues: 419 sheet: -0.97 (0.44), residues: 131 loop : -1.28 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1131 TYR 0.017 0.001 TYR A 664 PHE 0.012 0.002 PHE A 957 TRP 0.009 0.001 TRP A 466 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 9990) covalent geometry : angle 0.52399 / 0.30 (13839) hydrogen bonds : bond 0.05619 / 3.66 ( 415) hydrogen bonds : angle 4.59234 / 3.11 ( 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 86 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6197 (mp) REVERT: A 414 GLU cc_start: 0.8000 (tp30) cc_final: 0.7796 (tp30) REVERT: A 417 GLU cc_start: 0.7812 (tp30) cc_final: 0.7461 (tp30) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.2280 time to fit residues: 26.1055 Evaluate side-chains 80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 548 ILE 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 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 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4252 r_free = 0.4252 target = 0.154544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129559 restraints weight = 43627.000| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.42 r_work: 0.3898 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9990 Z= 0.151 Angle : 0.493 4.743 13839 Z= 0.287 Chirality : 0.038 0.236 1596 Planarity : 0.004 0.073 1459 Dihedral : 16.632 166.995 2321 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.79 % Favored : 94.00 % Rotamer: Outliers : 2.43 % Allowed : 16.18 % Favored : 81.39 % 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: -1.04 (0.27), residues: 950 helix: -0.01 (0.26), residues: 419 sheet: -0.93 (0.44), residues: 131 loop : -1.23 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1131 TYR 0.016 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/Z covalent geometry : bond 0.00335 / 0.15 ( 9990) covalent geometry : angle 0.49297 / 0.29 (13839) hydrogen bonds : bond 0.05105 / 3.34 ( 415) hydrogen bonds : angle 4.47542 / 3.03 ( 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 84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6196 (mp) REVERT: A 417 GLU cc_start: 0.7797 (tp30) cc_final: 0.7447 (tp30) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.2225 time to fit residues: 25.3992 Evaluate side-chains 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 548 ILE 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 886 LEU 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 1112 GLU Chi-restraints excluded: chain A residue 1141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.159197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133185 restraints weight = 43377.446| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.38 r_work: 0.3915 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9990 Z= 0.118 Angle : 0.476 4.934 13839 Z= 0.275 Chirality : 0.037 0.214 1596 Planarity : 0.004 0.081 1459 Dihedral : 16.569 163.016 2321 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.68 % Favored : 94.11 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % 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: -0.93 (0.28), residues: 950 helix: 0.12 (0.27), residues: 419 sheet: -0.97 (0.43), residues: 133 loop : -1.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1131 TYR 0.014 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/Z covalent geometry : bond 0.00258 / 0.12 ( 9990) covalent geometry : angle 0.47603 / 0.27 (13839) hydrogen bonds : bond 0.04701 / 3.10 ( 415) hydrogen bonds : angle 4.34539 / 2.94 ( 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 83 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6092 (mp) REVERT: A 417 GLU cc_start: 0.7705 (tp30) cc_final: 0.7409 (tp30) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.2482 time to fit residues: 27.8986 Evaluate side-chains 73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 1155 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 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: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.161187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.133962 restraints weight = 44431.467| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.52 r_work: 0.3914 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9990 Z= 0.117 Angle : 0.470 5.447 13839 Z= 0.270 Chirality : 0.037 0.202 1596 Planarity : 0.003 0.045 1459 Dihedral : 16.511 158.920 2321 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % 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: -0.73 (0.28), residues: 950 helix: 0.27 (0.27), residues: 420 sheet: -0.83 (0.46), residues: 123 loop : -1.08 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9990) covalent geometry : angle 0.47009 / 0.27 (13839) hydrogen bonds : bond 0.04525 / 2.98 ( 415) hydrogen bonds : angle 4.25824 / 2.88 ( 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 84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6011 (mp) REVERT: A 417 GLU cc_start: 0.7691 (tp30) cc_final: 0.7371 (tp30) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.2613 time to fit residues: 29.2678 Evaluate side-chains 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1155 SER 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: 0.6980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1007 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131753 restraints weight = 43435.669| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.31 r_work: 0.3900 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9990 Z= 0.178 Angle : 0.502 4.895 13839 Z= 0.288 Chirality : 0.038 0.209 1596 Planarity : 0.004 0.070 1459 Dihedral : 16.500 156.853 2321 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.63 % Favored : 93.16 % Rotamer: Outliers : 2.31 % Allowed : 16.30 % Favored : 81.39 % 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: -1.00 (0.28), residues: 950 helix: 0.09 (0.26), residues: 427 sheet: -1.04 (0.44), residues: 135 loop : -1.27 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 9990) covalent geometry : angle 0.50213 / 0.29 (13839) hydrogen bonds : bond 0.05029 / 3.29 ( 415) hydrogen bonds : angle 4.34998 / 2.95 ( 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: 20 poor density : 55 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6056 (mp) REVERT: A 417 GLU cc_start: 0.7742 (tp30) cc_final: 0.7424 (tp30) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.2353 time to fit residues: 24.9388 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 ------------------------------------------------------------------------------- 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 1068 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.158727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132114 restraints weight = 43583.436| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.31 r_work: 0.3906 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9990 Z= 0.147 Angle : 0.488 4.959 13839 Z= 0.280 Chirality : 0.037 0.195 1596 Planarity : 0.004 0.060 1459 Dihedral : 16.507 155.038 2321 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.74 % Favored : 93.05 % Rotamer: Outliers : 2.08 % Allowed : 16.42 % 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: -0.85 (0.28), residues: 950 helix: 0.21 (0.27), residues: 421 sheet: -0.98 (0.44), residues: 135 loop : -1.16 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 441 TYR 0.015 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/Z covalent geometry : bond 0.00329 / 0.15 ( 9990) covalent geometry : angle 0.48779 / 0.28 (13839) hydrogen bonds : bond 0.04791 / 3.14 ( 415) hydrogen bonds : angle 4.30538 / 2.92 ( 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 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6022 (mp) REVERT: A 417 GLU cc_start: 0.7742 (tp30) cc_final: 0.7421 (tp30) outliers start: 18 outliers final: 17 residues processed: 75 average time/residue: 0.2367 time to fit residues: 25.0448 Evaluate side-chains 74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 846 MET 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 Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1155 SER 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: 0.0000 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 847 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.158946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.132405 restraints weight = 43528.913| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.29 r_work: 0.3910 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9990 Z= 0.142 Angle : 0.484 4.967 13839 Z= 0.277 Chirality : 0.037 0.188 1596 Planarity : 0.004 0.061 1459 Dihedral : 16.484 153.023 2321 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.32 % Favored : 93.47 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % 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: -0.81 (0.28), residues: 950 helix: 0.24 (0.27), residues: 421 sheet: -0.91 (0.44), residues: 135 loop : -1.15 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 441 TYR 0.015 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/Z covalent geometry : bond 0.00317 / 0.14 ( 9990) covalent geometry : angle 0.48379 / 0.28 (13839) hydrogen bonds : bond 0.04704 / 3.09 ( 415) hydrogen bonds : angle 4.27304 / 2.90 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.82 seconds wall clock time: 76 minutes 13.07 seconds (4573.07 seconds total)