Starting phenix.real_space_refine on Thu Jan 16 17:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6l_50228/01_2025/9f6l_50228.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.101 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 Ca 2 9.91 5 Fe 4 7.16 5 P 26 5.49 5 S 53 5.16 5 C 6066 2.51 5 N 1647 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9639 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9098 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059} Chain breaks: 1 Chain: "P" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Unusual residues: {' CA': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4834 SG CYS A 651 38.003 19.250 53.220 1.00 99.09 S ATOM 4850 SG CYS A 654 36.437 17.492 47.221 1.00 98.87 S ATOM 4916 SG CYS A 663 42.008 16.185 49.846 1.00 97.49 S ATOM 5640 SG CYS A 747 41.526 21.844 48.347 1.00 94.19 S Time building chain proxies: 6.62, per 1000 atoms: 0.69 Number of scatterers: 9639 At special positions: 0 Unit cell: (103.66, 109.5, 109.5, 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) Fe 4 26.01 Ca 2 19.99 S 53 16.00 P 26 15.00 O 1841 8.00 N 1647 7.00 C 6066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " Number of angles added : 12 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 48.6% alpha, 17.2% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.576A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.522A pdb=" N SER A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.573A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 451 through 473 removed outlier: 3.804A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 4.014A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.842A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.157A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.722A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.825A pdb=" N CYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.802A pdb=" N LEU A 710 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 731 removed outlier: 4.582A pdb=" N ARG A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 730 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.222A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 4.168A pdb=" N ILE A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 905 removed outlier: 3.764A pdb=" N LEU A 897 " --> pdb=" O PRO A 893 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 899 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 901 " --> pdb=" O LEU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 994 removed outlier: 3.772A pdb=" N LYS A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 removed outlier: 4.269A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A1015 " --> pdb=" O ASP A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 3.558A pdb=" N TYR A1046 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.676A pdb=" N THR A1056 " --> pdb=" O THR A1052 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1097 through 1101 Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.507A pdb=" N LYS A1112 " --> pdb=" O HIS A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.010A pdb=" N ILE A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.771A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1175 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 7.126A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136 removed outlier: 6.681A pdb=" N SER A 156 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 131 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A 154 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR A 133 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 152 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG A 150 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 105 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 3.606A pdb=" N PHE A 320 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 274 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 361 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 539 removed outlier: 6.591A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 537 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG A 672 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR A 539 " --> pdb=" O GLN A 670 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN A 670 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 665 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 667 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.727A pdb=" N VAL A 867 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 858 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 624 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.633A pdb=" N GLY A 550 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 560 Processing sheet with id=AA9, first strand: chain 'A' and resid 875 through 879 removed outlier: 3.715A pdb=" N VAL A 888 " --> pdb=" O PHE A 878 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 907 through 913 removed outlier: 5.778A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1037 through 1038 removed outlier: 3.704A pdb=" N ARG A1037 " --> pdb=" O CYS A1076 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A1076 " --> pdb=" O ARG A1037 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080 435 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 4234 1.43 - 1.64: 5594 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 9918 Sorted by residual: bond pdb=" O4' DC P 31 " pdb=" C1' DC P 31 " ideal model delta sigma weight residual 1.414 1.391 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C2' DA T 16 " pdb=" C1' DA T 16 " ideal model delta sigma weight residual 1.525 1.504 0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C PHE A 675 " pdb=" N MET A 676 " ideal model delta sigma weight residual 1.340 1.399 -0.058 5.87e-02 2.90e+02 9.87e-01 bond pdb=" C2' DA P 22 " pdb=" C1' DA P 22 " ideal model delta sigma weight residual 1.525 1.505 0.020 2.00e-02 2.50e+03 9.58e-01 bond pdb=" C3' DA T 13 " pdb=" C2' DA T 13 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.02e-01 ... (remaining 9913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12204 1.01 - 2.02: 1016 2.02 - 3.02: 211 3.02 - 4.03: 69 4.03 - 5.04: 16 Bond angle restraints: 13516 Sorted by residual: angle pdb=" N TYR A 473 " pdb=" CA TYR A 473 " pdb=" C TYR A 473 " ideal model delta sigma weight residual 111.40 115.70 -4.30 1.22e+00 6.72e-01 1.24e+01 angle pdb=" C2' DG P 20 " pdb=" C1' DG P 20 " pdb=" N9 DG P 20 " ideal model delta sigma weight residual 113.50 118.13 -4.63 1.50e+00 4.44e-01 9.55e+00 angle pdb=" C2' DA P 21 " pdb=" C1' DA P 21 " pdb=" N9 DA P 21 " ideal model delta sigma weight residual 113.50 118.08 -4.58 1.50e+00 4.44e-01 9.31e+00 angle pdb=" N PHE A 905 " pdb=" CA PHE A 905 " pdb=" C PHE A 905 " ideal model delta sigma weight residual 111.69 115.33 -3.64 1.23e+00 6.61e-01 8.76e+00 angle pdb=" C LYS A1143 " pdb=" N ILE A1144 " pdb=" CA ILE A1144 " ideal model delta sigma weight residual 123.16 120.09 3.07 1.06e+00 8.90e-01 8.41e+00 ... (remaining 13511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5289 17.94 - 35.88: 458 35.88 - 53.82: 161 53.82 - 71.76: 33 71.76 - 89.70: 19 Dihedral angle restraints: 5960 sinusoidal: 2661 harmonic: 3299 Sorted by residual: dihedral pdb=" CA PHE A 905 " pdb=" C PHE A 905 " pdb=" N THR A 906 " pdb=" CA THR A 906 " ideal model delta harmonic sigma weight residual -180.00 -150.30 -29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG A 52 " pdb=" C ARG A 52 " pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL A1069 " pdb=" C VAL A1069 " pdb=" N LYS A1070 " pdb=" CA LYS A1070 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1196 0.052 - 0.104: 213 0.104 - 0.156: 44 0.156 - 0.208: 2 0.208 - 0.260: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C4' DA T 13 " pdb=" C5' DA T 13 " pdb=" O4' DA T 13 " pdb=" C3' DA T 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG A 749 " pdb=" N ARG A 749 " pdb=" C ARG A 749 " pdb=" CB ARG A 749 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CA PRO A1103 " pdb=" N PRO A1103 " pdb=" C PRO A1103 " pdb=" CB PRO A1103 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1453 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1138 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLY A1138 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY A1138 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A1139 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 26 " 0.022 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" N1 DT P 26 " -0.055 2.00e-02 2.50e+03 pdb=" C2 DT P 26 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DT P 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT P 26 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 26 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT P 26 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT P 26 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 26 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT P 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 476 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C PRO A 476 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 476 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 477 " -0.019 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 9703 3.24 - 3.80: 14215 3.80 - 4.35: 18138 4.35 - 4.90: 30515 Nonbonded interactions: 72788 Sorted by model distance: nonbonded pdb=" OP1 DC P 31 " pdb="CA CA A1303 " model vdw 2.141 2.510 nonbonded pdb=" OP1 DC P 31 " pdb="CA CA A1302 " model vdw 2.151 2.510 nonbonded pdb=" O5' DC P 31 " pdb="CA CA A1303 " model vdw 2.202 2.510 nonbonded pdb=" OE2 GLU A 223 " pdb=" NH2 ARG A 231 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR A 528 " pdb=" OD1 ASP A 530 " model vdw 2.257 3.040 ... (remaining 72783 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 group one per residue 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: 0.480 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9918 Z= 0.182 Angle : 0.666 5.041 13516 Z= 0.409 Chirality : 0.042 0.260 1456 Planarity : 0.009 0.084 1655 Dihedral : 16.408 89.702 3824 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1114 helix: -0.95 (0.20), residues: 452 sheet: 0.49 (0.37), residues: 181 loop : -0.70 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP A 865 HIS 0.007 0.002 HIS A 67 PHE 0.023 0.004 PHE A 367 TYR 0.028 0.005 TYR A 726 ARG 0.018 0.003 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8145 (m-30) cc_final: 0.7334 (p0) REVERT: A 119 PHE cc_start: 0.8582 (t80) cc_final: 0.8381 (t80) REVERT: A 447 MET cc_start: 0.9296 (mpp) cc_final: 0.8454 (mpp) REVERT: A 818 TYR cc_start: 0.8472 (t80) cc_final: 0.8004 (t80) REVERT: A 878 PHE cc_start: 0.7505 (m-80) cc_final: 0.6674 (m-10) REVERT: A 896 MET cc_start: 0.8941 (tmm) cc_final: 0.8626 (tmm) REVERT: A 952 LEU cc_start: 0.9080 (mt) cc_final: 0.8745 (mp) REVERT: A 974 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6649 (tptt) REVERT: A 1087 SER cc_start: 0.8774 (m) cc_final: 0.8542 (p) REVERT: A 1135 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3030 time to fit residues: 63.4059 Evaluate side-chains 77 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 342 HIS A 511 HIS A 772 HIS A1163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084881 restraints weight = 22615.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087153 restraints weight = 13716.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088708 restraints weight = 9844.758| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9918 Z= 0.177 Angle : 0.613 11.321 13516 Z= 0.333 Chirality : 0.042 0.160 1456 Planarity : 0.005 0.034 1655 Dihedral : 15.768 82.030 1509 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.41 % Allowed : 9.48 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1114 helix: 0.93 (0.23), residues: 465 sheet: 0.63 (0.39), residues: 180 loop : -0.19 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 671 HIS 0.003 0.001 HIS A 67 PHE 0.022 0.002 PHE A 596 TYR 0.015 0.001 TYR A 827 ARG 0.006 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8011 (m-30) cc_final: 0.7498 (p0) REVERT: A 119 PHE cc_start: 0.8530 (t80) cc_final: 0.8327 (t80) REVERT: A 285 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 383 MET cc_start: 0.8710 (tpp) cc_final: 0.8258 (ttm) REVERT: A 405 MET cc_start: 0.9238 (tpp) cc_final: 0.8916 (mmm) REVERT: A 444 MET cc_start: 0.8591 (mmm) cc_final: 0.8222 (mmm) REVERT: A 447 MET cc_start: 0.9395 (mpp) cc_final: 0.8828 (mpp) REVERT: A 471 MET cc_start: 0.8525 (tpp) cc_final: 0.8191 (tpp) REVERT: A 630 MET cc_start: 0.8440 (ttp) cc_final: 0.8174 (ttp) REVERT: A 688 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.8674 (t-90) REVERT: A 896 MET cc_start: 0.9009 (tmm) cc_final: 0.8615 (tmm) REVERT: A 952 LEU cc_start: 0.9145 (mt) cc_final: 0.8737 (mp) REVERT: A 953 LYS cc_start: 0.8679 (mppt) cc_final: 0.8374 (mppt) REVERT: A 1024 MET cc_start: 0.7835 (ttm) cc_final: 0.7337 (ttm) REVERT: A 1039 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7053 (tpt) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.2393 time to fit residues: 33.8170 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.084682 restraints weight = 22711.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087051 restraints weight = 13450.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088592 restraints weight = 9528.695| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9918 Z= 0.155 Angle : 0.552 13.018 13516 Z= 0.293 Chirality : 0.040 0.188 1456 Planarity : 0.004 0.040 1655 Dihedral : 15.337 76.921 1509 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.51 % Allowed : 10.48 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1114 helix: 1.55 (0.24), residues: 469 sheet: 0.58 (0.38), residues: 195 loop : -0.16 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 708 PHE 0.016 0.001 PHE A 596 TYR 0.011 0.001 TYR A 827 ARG 0.005 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7996 (m-30) cc_final: 0.7673 (p0) REVERT: A 119 PHE cc_start: 0.8573 (t80) cc_final: 0.8355 (t80) REVERT: A 278 THR cc_start: 0.8590 (p) cc_final: 0.8376 (p) REVERT: A 285 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6674 (t80) REVERT: A 294 MET cc_start: 0.8361 (mtp) cc_final: 0.7934 (mtm) REVERT: A 383 MET cc_start: 0.8678 (tpp) cc_final: 0.8272 (ttm) REVERT: A 471 MET cc_start: 0.8847 (tpp) cc_final: 0.8132 (tpp) REVERT: A 630 MET cc_start: 0.8491 (ttp) cc_final: 0.8282 (ttp) REVERT: A 645 MET cc_start: 0.8662 (mpt) cc_final: 0.8229 (mpp) REVERT: A 896 MET cc_start: 0.9030 (tmm) cc_final: 0.8700 (tmm) REVERT: A 1024 MET cc_start: 0.7971 (ttm) cc_final: 0.7557 (ttm) REVERT: A 1107 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8298 (mmtm) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.2197 time to fit residues: 31.7317 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084425 restraints weight = 22555.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086681 restraints weight = 13486.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088273 restraints weight = 9643.888| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9918 Z= 0.149 Angle : 0.524 13.331 13516 Z= 0.277 Chirality : 0.040 0.140 1456 Planarity : 0.004 0.044 1655 Dihedral : 15.210 77.561 1509 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.61 % Allowed : 12.10 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1114 helix: 1.92 (0.24), residues: 467 sheet: 0.71 (0.38), residues: 207 loop : -0.18 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 671 HIS 0.002 0.001 HIS A 708 PHE 0.016 0.001 PHE A1122 TYR 0.011 0.001 TYR A 298 ARG 0.005 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7922 (m-30) cc_final: 0.7678 (p0) REVERT: A 119 PHE cc_start: 0.8605 (t80) cc_final: 0.8378 (t80) REVERT: A 285 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6597 (t80) REVERT: A 383 MET cc_start: 0.8722 (tpp) cc_final: 0.8275 (ttm) REVERT: A 471 MET cc_start: 0.8891 (tpp) cc_final: 0.8128 (tpp) REVERT: A 582 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 630 MET cc_start: 0.8384 (ttp) cc_final: 0.8166 (ttp) REVERT: A 645 MET cc_start: 0.8594 (mpt) cc_final: 0.8223 (mpp) REVERT: A 896 MET cc_start: 0.9042 (tmm) cc_final: 0.8733 (tmm) REVERT: A 1024 MET cc_start: 0.7915 (ttm) cc_final: 0.7422 (ttm) REVERT: A 1107 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8331 (mmtm) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.2170 time to fit residues: 29.8401 Evaluate side-chains 79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080228 restraints weight = 22975.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082372 restraints weight = 14106.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083808 restraints weight = 10247.248| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9918 Z= 0.258 Angle : 0.598 13.382 13516 Z= 0.316 Chirality : 0.042 0.140 1456 Planarity : 0.005 0.049 1655 Dihedral : 15.302 81.143 1509 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 12.20 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1114 helix: 1.94 (0.24), residues: 462 sheet: 0.67 (0.38), residues: 204 loop : -0.34 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 369 HIS 0.005 0.001 HIS A 239 PHE 0.017 0.002 PHE A 596 TYR 0.021 0.002 TYR A 910 ARG 0.004 0.000 ARG A1160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8078 (m-30) cc_final: 0.7661 (p0) REVERT: A 119 PHE cc_start: 0.8635 (t80) cc_final: 0.8308 (t80) REVERT: A 285 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6813 (t80) REVERT: A 383 MET cc_start: 0.8690 (tpp) cc_final: 0.8250 (ttm) REVERT: A 447 MET cc_start: 0.9298 (mpp) cc_final: 0.8366 (mtp) REVERT: A 471 MET cc_start: 0.8955 (tpp) cc_final: 0.8239 (tpp) REVERT: A 582 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 630 MET cc_start: 0.8467 (ttp) cc_final: 0.8248 (ttp) REVERT: A 896 MET cc_start: 0.9080 (tmm) cc_final: 0.8703 (tmm) REVERT: A 1039 MET cc_start: 0.7999 (tpt) cc_final: 0.7381 (tpt) REVERT: A 1107 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8342 (mmtm) outliers start: 24 outliers final: 13 residues processed: 87 average time/residue: 0.2270 time to fit residues: 28.6079 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.084363 restraints weight = 22562.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086413 restraints weight = 14659.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087380 restraints weight = 10154.233| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9918 Z= 0.170 Angle : 0.530 13.621 13516 Z= 0.278 Chirality : 0.040 0.134 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.236 79.580 1509 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.92 % Allowed : 13.10 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1114 helix: 2.14 (0.24), residues: 467 sheet: 0.59 (0.37), residues: 212 loop : -0.29 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.002 0.001 HIS A 242 PHE 0.015 0.001 PHE A1122 TYR 0.011 0.001 TYR A 910 ARG 0.005 0.000 ARG A1077 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 119 PHE cc_start: 0.8624 (t80) cc_final: 0.8374 (t80) REVERT: A 285 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6774 (t80) REVERT: A 383 MET cc_start: 0.8751 (tpp) cc_final: 0.8264 (ttm) REVERT: A 447 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8242 (mtt) REVERT: A 471 MET cc_start: 0.8835 (tpp) cc_final: 0.8088 (tpp) REVERT: A 582 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9141 (mm) REVERT: A 645 MET cc_start: 0.8804 (mpt) cc_final: 0.8541 (mpp) REVERT: A 896 MET cc_start: 0.8933 (tmm) cc_final: 0.8617 (tmm) REVERT: A 1107 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8354 (mmtm) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.2064 time to fit residues: 26.5556 Evaluate side-chains 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 chunk 32 optimal weight: 9.9990 chunk 103 optimal weight: 0.0060 chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 772 HIS A 980 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085124 restraints weight = 22477.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087498 restraints weight = 13483.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089111 restraints weight = 9623.522| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9918 Z= 0.126 Angle : 0.503 14.554 13516 Z= 0.260 Chirality : 0.039 0.133 1456 Planarity : 0.004 0.044 1655 Dihedral : 15.003 76.000 1509 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.21 % Allowed : 14.01 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1114 helix: 2.27 (0.24), residues: 468 sheet: 0.60 (0.37), residues: 208 loop : -0.30 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.006 0.001 HIS A 144 PHE 0.013 0.001 PHE A1122 TYR 0.011 0.001 TYR A 298 ARG 0.004 0.000 ARG A1077 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 447 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8303 (mtt) REVERT: A 471 MET cc_start: 0.8880 (tpp) cc_final: 0.8069 (tpp) REVERT: A 582 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8982 (mm) REVERT: A 645 MET cc_start: 0.8788 (mpt) cc_final: 0.8537 (mpp) REVERT: A 722 ARG cc_start: 0.5994 (mtt-85) cc_final: 0.5793 (mtt-85) REVERT: A 896 MET cc_start: 0.8959 (tmm) cc_final: 0.8601 (tmm) REVERT: A 1107 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8351 (mmtm) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.2110 time to fit residues: 28.5550 Evaluate side-chains 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085796 restraints weight = 23579.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088157 restraints weight = 14022.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089765 restraints weight = 10045.171| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9918 Z= 0.191 Angle : 0.534 13.580 13516 Z= 0.278 Chirality : 0.040 0.133 1456 Planarity : 0.004 0.043 1655 Dihedral : 14.973 76.565 1509 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.41 % Allowed : 14.62 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1114 helix: 2.34 (0.24), residues: 468 sheet: 0.56 (0.37), residues: 208 loop : -0.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 369 HIS 0.002 0.001 HIS A 242 PHE 0.020 0.001 PHE A 119 TYR 0.014 0.001 TYR A 910 ARG 0.003 0.000 ARG A1077 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 447 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: A 471 MET cc_start: 0.8779 (tpp) cc_final: 0.8059 (tpp) REVERT: A 582 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9062 (mm) REVERT: A 645 MET cc_start: 0.8811 (mpt) cc_final: 0.8565 (mpp) REVERT: A 722 ARG cc_start: 0.6028 (mtt-85) cc_final: 0.5820 (mtt-85) REVERT: A 896 MET cc_start: 0.8925 (tmm) cc_final: 0.8591 (tmm) REVERT: A 1107 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8371 (mmtm) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 0.2120 time to fit residues: 26.4227 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.0040 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087320 restraints weight = 23224.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089709 restraints weight = 13833.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091286 restraints weight = 9906.989| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9918 Z= 0.140 Angle : 0.526 14.188 13516 Z= 0.269 Chirality : 0.039 0.131 1456 Planarity : 0.004 0.043 1655 Dihedral : 14.909 75.422 1509 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.31 % Allowed : 15.32 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1114 helix: 2.42 (0.24), residues: 468 sheet: 0.53 (0.37), residues: 211 loop : -0.26 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.002 0.000 HIS A 404 PHE 0.044 0.001 PHE A 119 TYR 0.011 0.001 TYR A 298 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6752 (t80) REVERT: A 299 MET cc_start: 0.8747 (tpp) cc_final: 0.8489 (tpp) REVERT: A 447 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: A 471 MET cc_start: 0.8761 (tpp) cc_final: 0.8059 (tpp) REVERT: A 582 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9035 (mm) REVERT: A 645 MET cc_start: 0.8775 (mpt) cc_final: 0.8513 (mpp) REVERT: A 722 ARG cc_start: 0.6025 (mtt-85) cc_final: 0.5815 (mtt-85) REVERT: A 896 MET cc_start: 0.8878 (tmm) cc_final: 0.8553 (tmm) REVERT: A 1107 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8366 (mmtm) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.2194 time to fit residues: 27.1114 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085429 restraints weight = 23302.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087742 restraints weight = 13917.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089286 restraints weight = 10010.837| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9918 Z= 0.193 Angle : 0.546 13.682 13516 Z= 0.281 Chirality : 0.040 0.132 1456 Planarity : 0.004 0.044 1655 Dihedral : 14.912 75.759 1509 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.31 % Allowed : 15.12 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1114 helix: 2.41 (0.24), residues: 469 sheet: 0.62 (0.37), residues: 207 loop : -0.34 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE A1122 TYR 0.014 0.001 TYR A 910 ARG 0.003 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6855 (t80) REVERT: A 299 MET cc_start: 0.8742 (tpp) cc_final: 0.8500 (tpp) REVERT: A 447 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8194 (mtt) REVERT: A 471 MET cc_start: 0.8775 (tpp) cc_final: 0.8089 (tpp) REVERT: A 582 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 645 MET cc_start: 0.8734 (mpt) cc_final: 0.8485 (mpp) REVERT: A 722 ARG cc_start: 0.6162 (mtt-85) cc_final: 0.5954 (mtt-85) REVERT: A 896 MET cc_start: 0.8902 (tmm) cc_final: 0.8576 (tmm) REVERT: A 1107 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8372 (mmtm) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.2001 time to fit residues: 23.7146 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.0470 chunk 99 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088001 restraints weight = 23297.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090432 restraints weight = 13517.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092036 restraints weight = 9576.399| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9918 Z= 0.137 Angle : 0.522 14.663 13516 Z= 0.267 Chirality : 0.039 0.131 1456 Planarity : 0.004 0.043 1655 Dihedral : 14.827 75.955 1509 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 15.73 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1114 helix: 2.49 (0.24), residues: 467 sheet: 0.40 (0.36), residues: 216 loop : -0.23 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.002 0.000 HIS A 404 PHE 0.011 0.001 PHE A1122 TYR 0.012 0.001 TYR A 956 ARG 0.002 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.68 seconds wall clock time: 48 minutes 23.16 seconds (2903.16 seconds total)