Starting phenix.real_space_refine on Wed Sep 25 06:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_50228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_50228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_50228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_50228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6l_50228/09_2024/9f6l_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.64, per 1000 atoms: 0.59 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: 2.68 Conformation dependent library (CDL) restraints added in 1.0 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: 3.09 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: 4.20 Time building geometry restraints manager: 3.07 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: 0.600 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.093 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: 0.2762 time to fit residues: 57.6816 Evaluate side-chains 77 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7993 (m-30) cc_final: 0.7471 (p0) REVERT: A 285 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 383 MET cc_start: 0.8721 (tpp) cc_final: 0.8209 (ttm) REVERT: A 405 MET cc_start: 0.9257 (tpp) cc_final: 0.8948 (mmm) REVERT: A 444 MET cc_start: 0.8676 (mmm) cc_final: 0.8305 (mmm) REVERT: A 447 MET cc_start: 0.9356 (mpp) cc_final: 0.8854 (mpp) REVERT: A 471 MET cc_start: 0.8552 (tpp) cc_final: 0.8209 (tpp) REVERT: A 630 MET cc_start: 0.8368 (ttp) cc_final: 0.8116 (ttp) REVERT: A 688 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8658 (t-90) REVERT: A 896 MET cc_start: 0.9012 (tmm) cc_final: 0.8619 (tmm) REVERT: A 952 LEU cc_start: 0.9137 (mt) cc_final: 0.8760 (mp) REVERT: A 953 LYS cc_start: 0.8653 (mppt) cc_final: 0.8328 (mppt) REVERT: A 1024 MET cc_start: 0.7786 (ttm) cc_final: 0.7310 (ttm) REVERT: A 1039 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7005 (tpt) REVERT: A 1087 SER cc_start: 0.8804 (m) cc_final: 0.8598 (p) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.2342 time to fit residues: 32.9899 Evaluate side-chains 84 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9918 Z= 0.234 Angle : 0.587 12.663 13516 Z= 0.316 Chirality : 0.042 0.179 1456 Planarity : 0.005 0.043 1655 Dihedral : 15.464 79.004 1509 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.12 % Allowed : 10.58 % Favored : 87.30 % 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: 0.83 (0.26), residues: 1114 helix: 1.38 (0.24), residues: 470 sheet: 0.60 (0.38), residues: 193 loop : -0.26 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 865 HIS 0.004 0.001 HIS A 708 PHE 0.031 0.002 PHE A 119 TYR 0.016 0.001 TYR A 910 ARG 0.005 0.000 ARG A1160 *********************** 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 97 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7904 (m-30) cc_final: 0.7547 (p0) REVERT: A 278 THR cc_start: 0.8786 (p) cc_final: 0.8471 (p) REVERT: A 285 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6737 (t80) REVERT: A 294 MET cc_start: 0.8307 (mtp) cc_final: 0.7909 (mtm) REVERT: A 383 MET cc_start: 0.8691 (tpp) cc_final: 0.8267 (ttm) REVERT: A 405 MET cc_start: 0.9349 (tpp) cc_final: 0.9106 (mmm) REVERT: A 447 MET cc_start: 0.9287 (mpp) cc_final: 0.8589 (mpp) REVERT: A 471 MET cc_start: 0.8877 (tpp) cc_final: 0.8209 (tpp) REVERT: A 582 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9202 (mm) REVERT: A 630 MET cc_start: 0.8382 (ttp) cc_final: 0.8177 (ttp) REVERT: A 645 MET cc_start: 0.8631 (mpt) cc_final: 0.8236 (mpp) REVERT: A 688 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (t-90) REVERT: A 896 MET cc_start: 0.9038 (tmm) cc_final: 0.8689 (tmm) REVERT: A 1024 MET cc_start: 0.7877 (ttm) cc_final: 0.7411 (ttm) REVERT: A 1107 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8358 (mmtm) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.2197 time to fit residues: 28.9837 Evaluate side-chains 82 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 464 VAL Chi-restraints excluded: chain A residue 514 ILE 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 688 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9918 Z= 0.310 Angle : 0.626 13.667 13516 Z= 0.338 Chirality : 0.044 0.145 1456 Planarity : 0.005 0.055 1655 Dihedral : 15.557 82.448 1509 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.62 % Allowed : 11.39 % Favored : 85.99 % 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: 0.89 (0.26), residues: 1114 helix: 1.59 (0.24), residues: 461 sheet: 0.58 (0.38), residues: 209 loop : -0.41 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 62 HIS 0.005 0.001 HIS A 242 PHE 0.036 0.002 PHE A 119 TYR 0.022 0.002 TYR A 910 ARG 0.008 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 fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 1.141 Fit side-chains REVERT: A 83 ASP cc_start: 0.7888 (m-30) cc_final: 0.7500 (p0) REVERT: A 285 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6703 (t80) REVERT: A 383 MET cc_start: 0.8762 (tpp) cc_final: 0.8328 (ttm) REVERT: A 405 MET cc_start: 0.9413 (tpp) cc_final: 0.9171 (mmm) REVERT: A 471 MET cc_start: 0.9011 (tpp) cc_final: 0.8366 (tpp) REVERT: A 688 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8720 (t-90) REVERT: A 896 MET cc_start: 0.9093 (tmm) cc_final: 0.8729 (tmm) REVERT: A 1039 MET cc_start: 0.7894 (tpt) cc_final: 0.7283 (tpt) REVERT: A 1107 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8296 (mmtm) outliers start: 26 outliers final: 12 residues processed: 91 average time/residue: 0.2206 time to fit residues: 28.8763 Evaluate side-chains 75 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 218 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 979 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9918 Z= 0.163 Angle : 0.536 11.890 13516 Z= 0.286 Chirality : 0.040 0.147 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.479 80.804 1509 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.41 % Allowed : 13.51 % Favored : 85.08 % 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: 1.13 (0.26), residues: 1114 helix: 1.88 (0.24), residues: 466 sheet: 0.61 (0.37), residues: 213 loop : -0.37 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 369 HIS 0.002 0.001 HIS A 242 PHE 0.032 0.001 PHE A 119 TYR 0.014 0.001 TYR A 397 ARG 0.004 0.000 ARG A 114 *********************** 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 89 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7939 (m-30) cc_final: 0.7565 (p0) REVERT: A 221 MET cc_start: 0.9011 (ptp) cc_final: 0.8733 (ptt) REVERT: A 285 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6826 (t80) REVERT: A 383 MET cc_start: 0.8710 (tpp) cc_final: 0.8261 (ttm) REVERT: A 405 MET cc_start: 0.9365 (tpp) cc_final: 0.9158 (mmm) REVERT: A 447 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: A 471 MET cc_start: 0.9024 (tpp) cc_final: 0.8272 (tpp) REVERT: A 582 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9163 (mm) REVERT: A 645 MET cc_start: 0.8825 (mpt) cc_final: 0.8553 (mpp) REVERT: A 688 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8660 (t-90) REVERT: A 896 MET cc_start: 0.9089 (tmm) cc_final: 0.8727 (tmm) REVERT: A 1107 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8308 (mmtm) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.2046 time to fit residues: 26.5173 Evaluate side-chains 81 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 723 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0030 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 105 optimal weight: 5.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9918 Z= 0.136 Angle : 0.515 13.042 13516 Z= 0.269 Chirality : 0.039 0.141 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.219 77.719 1509 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.71 % Allowed : 13.61 % Favored : 84.68 % 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: 2.19 (0.24), residues: 467 sheet: 0.63 (0.37), residues: 215 loop : -0.38 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.009 0.001 HIS A 144 PHE 0.021 0.001 PHE A 119 TYR 0.010 0.001 TYR A 827 ARG 0.003 0.000 ARG A 114 *********************** 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 104 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7832 (m-30) cc_final: 0.7623 (p0) REVERT: A 285 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6919 (t80) REVERT: A 383 MET cc_start: 0.8696 (tpp) cc_final: 0.8473 (ttp) REVERT: A 447 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: A 471 MET cc_start: 0.8999 (tpp) cc_final: 0.8211 (tpp) REVERT: A 582 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 645 MET cc_start: 0.8860 (mpt) cc_final: 0.8583 (mpp) REVERT: A 722 ARG cc_start: 0.5833 (mtt-85) cc_final: 0.5621 (mtt-85) REVERT: A 896 MET cc_start: 0.9045 (tmm) cc_final: 0.8680 (tmm) REVERT: A 1107 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (mmtm) outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 0.1886 time to fit residues: 27.5506 Evaluate side-chains 89 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 815 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9918 Z= 0.158 Angle : 0.529 12.608 13516 Z= 0.274 Chirality : 0.039 0.143 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.119 77.567 1509 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 14.92 % Favored : 83.67 % 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: 1.38 (0.26), residues: 1114 helix: 2.29 (0.24), residues: 467 sheet: 0.50 (0.37), residues: 209 loop : -0.37 (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 0.014 0.001 PHE A1122 TYR 0.011 0.001 TYR A 298 ARG 0.003 0.000 ARG A 114 *********************** 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 92 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7861 (m-30) cc_final: 0.7646 (p0) REVERT: A 285 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 383 MET cc_start: 0.8710 (tpp) cc_final: 0.8459 (ttp) REVERT: A 447 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8318 (mtt) REVERT: A 471 MET cc_start: 0.8993 (tpp) cc_final: 0.8229 (tpp) REVERT: A 582 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 645 MET cc_start: 0.8839 (mpt) cc_final: 0.8580 (mpp) REVERT: A 896 MET cc_start: 0.9035 (tmm) cc_final: 0.8659 (tmm) REVERT: A 1107 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8346 (mmtm) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.1940 time to fit residues: 25.0671 Evaluate side-chains 83 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 911 GLN A 980 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9918 Z= 0.299 Angle : 0.609 11.948 13516 Z= 0.322 Chirality : 0.042 0.143 1456 Planarity : 0.005 0.049 1655 Dihedral : 15.323 80.914 1509 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.12 % Allowed : 15.32 % Favored : 82.56 % 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: 1.04 (0.26), residues: 1114 helix: 2.01 (0.24), residues: 466 sheet: 0.29 (0.37), residues: 209 loop : -0.53 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 671 HIS 0.005 0.001 HIS A 242 PHE 0.017 0.002 PHE A 104 TYR 0.022 0.002 TYR A 910 ARG 0.004 0.000 ARG A 37 *********************** 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 91 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7942 (m-30) cc_final: 0.7549 (p0) REVERT: A 285 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6772 (t80) REVERT: A 383 MET cc_start: 0.8788 (tpp) cc_final: 0.8346 (ttm) REVERT: A 447 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: A 471 MET cc_start: 0.9021 (tpp) cc_final: 0.8260 (tpp) REVERT: A 582 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 645 MET cc_start: 0.8839 (mpt) cc_final: 0.8591 (mpp) REVERT: A 896 MET cc_start: 0.9060 (tmm) cc_final: 0.8661 (tmm) REVERT: A 1107 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8358 (mmtm) outliers start: 21 outliers final: 10 residues processed: 84 average time/residue: 0.1830 time to fit residues: 23.2915 Evaluate side-chains 82 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU 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 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 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 101 optimal weight: 0.0770 chunk 104 optimal weight: 0.0060 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9918 Z= 0.139 Angle : 0.538 13.434 13516 Z= 0.280 Chirality : 0.039 0.139 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.200 77.705 1509 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.51 % Allowed : 15.73 % Favored : 82.76 % 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: 1.32 (0.26), residues: 1114 helix: 2.28 (0.24), residues: 467 sheet: 0.40 (0.36), residues: 217 loop : -0.42 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.003 0.000 HIS A 404 PHE 0.013 0.001 PHE A1122 TYR 0.017 0.001 TYR A 224 ARG 0.004 0.000 ARG A 222 *********************** 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 89 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7955 (m-30) cc_final: 0.7613 (p0) REVERT: A 285 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6793 (t80) REVERT: A 383 MET cc_start: 0.8739 (tpp) cc_final: 0.8500 (ttp) REVERT: A 447 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8233 (mtt) REVERT: A 471 MET cc_start: 0.8989 (tpp) cc_final: 0.8193 (tpp) REVERT: A 506 MET cc_start: 0.9095 (mmm) cc_final: 0.8725 (mmt) REVERT: A 582 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8996 (mm) REVERT: A 645 MET cc_start: 0.8795 (mpt) cc_final: 0.8529 (mpp) REVERT: A 896 MET cc_start: 0.9015 (tmm) cc_final: 0.8598 (tmm) REVERT: A 1107 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8049 (mmtm) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.1725 time to fit residues: 22.7864 Evaluate side-chains 82 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 723 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 Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9918 Z= 0.155 Angle : 0.542 13.657 13516 Z= 0.279 Chirality : 0.039 0.143 1456 Planarity : 0.004 0.044 1655 Dihedral : 15.059 76.108 1509 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.11 % Allowed : 16.33 % Favored : 82.56 % 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: 1.39 (0.26), residues: 1114 helix: 2.34 (0.24), residues: 469 sheet: 0.37 (0.36), residues: 215 loop : -0.34 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 671 HIS 0.002 0.000 HIS A 404 PHE 0.011 0.001 PHE A1122 TYR 0.011 0.001 TYR A 298 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 81 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7921 (m-30) cc_final: 0.7642 (p0) REVERT: A 285 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6808 (t80) REVERT: A 383 MET cc_start: 0.8721 (tpp) cc_final: 0.8516 (ttp) REVERT: A 447 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: A 471 MET cc_start: 0.8979 (tpp) cc_final: 0.8209 (tpp) REVERT: A 506 MET cc_start: 0.9091 (mmm) cc_final: 0.8726 (mmt) REVERT: A 582 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 645 MET cc_start: 0.8808 (mpt) cc_final: 0.8510 (mpp) REVERT: A 896 MET cc_start: 0.9008 (tmm) cc_final: 0.8597 (tmm) REVERT: A 1107 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8360 (mmtm) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1980 time to fit residues: 23.2551 Evaluate side-chains 79 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 610 LEU Chi-restraints excluded: chain A residue 723 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 911 GLN A 980 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088551 restraints weight = 23004.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091020 restraints weight = 13330.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.092641 restraints weight = 9403.501| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9918 Z= 0.129 Angle : 0.531 14.706 13516 Z= 0.270 Chirality : 0.039 0.141 1456 Planarity : 0.004 0.044 1655 Dihedral : 14.986 77.510 1509 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 15.83 % Favored : 83.06 % 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: 1.49 (0.26), residues: 1114 helix: 2.41 (0.24), residues: 468 sheet: 0.40 (0.36), residues: 215 loop : -0.26 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.002 0.000 HIS A 404 PHE 0.010 0.001 PHE A 699 TYR 0.011 0.001 TYR A1133 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: 1829.58 seconds wall clock time: 33 minutes 31.03 seconds (2011.03 seconds total)