Starting phenix.real_space_refine on Wed Aug 5 12:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6i_50225/08_2026/9f6i_50225.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.165 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 1 9.91 5 Fe 4 7.16 5 P 35 5.49 5 S 53 5.16 5 C 6133 2.51 5 N 1667 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9781 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9091 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' CA': 1, 'DDS': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4827 SG CYS A 651 37.998 18.768 53.773 1.00 16.44 S ATOM 4843 SG CYS A 654 36.397 16.440 47.735 1.00 16.34 S ATOM 4909 SG CYS A 663 42.250 15.217 49.953 1.00 17.89 S ATOM 5633 SG CYS A 747 41.376 20.889 48.607 1.00 17.89 S Time building chain proxies: 2.52, per 1000 atoms: 0.26 Number of scatterers: 9781 At special positions: 0 Unit cell: (103.66, 105.12, 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 1 19.99 S 53 16.00 P 35 15.00 O 1888 8.00 N 1667 7.00 C 6133 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: 0.98 Conformation dependent library (CDL) restraints added in 340.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " 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: 46 helices and 13 sheets defined 50.5% alpha, 15.4% beta 12 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.07 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: 3.869A pdb=" N LYS A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.542A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.975A pdb=" N ALA A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 253' Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.564A pdb=" N PHE A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.709A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 406 through 412 removed outlier: 4.130A pdb=" N TRP A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.221A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 473 removed outlier: 3.943A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 4.137A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 479 " --> pdb=" O HIS A 475 " (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: 3.870A pdb=" N LEU A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 505 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.783A pdb=" N VAL A 593 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 613 removed outlier: 4.009A 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 654 removed outlier: 3.598A pdb=" N CYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 731 Processing helix chain 'A' and resid 752 through 786 removed outlier: 3.556A pdb=" N TYR A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 819 removed outlier: 4.530A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 854 removed outlier: 3.553A pdb=" N CYS A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.733A pdb=" N LEU A 897 " --> pdb=" O PRO A 893 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 903 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 979 through 994 removed outlier: 3.569A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 removed outlier: 3.586A pdb=" N ALA A1007 " --> pdb=" O TYR A1003 " (cutoff:3.500A) removed outlier: 4.154A 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: 3.585A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 removed outlier: 3.851A pdb=" N LEU A1029 " --> pdb=" O PRO A1025 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 3.903A pdb=" N TYR A1046 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 4.264A pdb=" N VAL A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1091 Processing helix chain 'A' and resid 1097 through 1101 Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.568A pdb=" N HIS A1108 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.706A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1135 " --> pdb=" O ASP A1131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1151 Processing helix chain 'A' and resid 1164 through 1175 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 99 removed outlier: 3.516A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.371A 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: 7.250A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 220 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 3.810A pdb=" N PHE A 320 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (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 536 removed outlier: 6.621A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.598A pdb=" N TYR A 956 " --> pdb=" O LYS A 969 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 560 Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 859 removed outlier: 6.480A pdb=" N VAL A 867 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS A 624 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 645 through 646 removed outlier: 4.334A pdb=" N THR A 745 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 665 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB2, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AB3, first strand: chain 'A' and resid 911 through 913 Processing sheet with id=AB4, first strand: chain 'A' and resid 1078 through 1080 444 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.26 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: 4309 1.43 - 1.64: 5677 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 10076 Sorted by residual: bond pdb=" O3B DDS A1302 " pdb=" PG DDS A1302 " ideal model delta sigma weight residual 1.745 1.619 0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C1' DT P 30 " pdb=" N1 DT P 30 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" C3' DC P 24 " pdb=" C2' DC P 24 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" O3A DDS A1302 " pdb=" PB DDS A1302 " ideal model delta sigma weight residual 1.674 1.602 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C3' DG P 28 " pdb=" C2' DG P 28 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 ... (remaining 10071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 12736 1.26 - 2.52: 836 2.52 - 3.78: 156 3.78 - 5.04: 25 5.04 - 6.31: 9 Bond angle restraints: 13762 Sorted by residual: angle pdb=" C4' DG P 28 " pdb=" O4' DG P 28 " pdb=" C1' DG P 28 " ideal model delta sigma weight residual 110.10 105.31 4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N3 DT P 30 " pdb=" C4 DT P 30 " pdb=" O4 DT P 30 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4' DC P 31 " pdb=" C4' DC P 31 " pdb=" C3' DC P 31 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4 DT P 30 " pdb=" C4 DT P 30 " pdb=" C5 DT P 30 " ideal model delta sigma weight residual 124.90 121.87 3.03 7.00e-01 2.04e+00 1.88e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 13757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 5771 31.52 - 63.04: 249 63.04 - 94.55: 24 94.55 - 126.07: 2 126.07 - 157.59: 4 Dihedral angle restraints: 6050 sinusoidal: 2751 harmonic: 3299 Sorted by residual: dihedral pdb=" CA ARG A1082 " pdb=" C ARG A1082 " pdb=" N LYS A1083 " pdb=" CA LYS A1083 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA THR A 290 " pdb=" C THR A 290 " pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ILE A1145 " pdb=" C ILE A1145 " pdb=" N THR A1146 " pdb=" CA THR A1146 " ideal model delta harmonic sigma weight residual 180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1007 0.039 - 0.077: 325 0.077 - 0.116: 108 0.116 - 0.154: 37 0.154 - 0.193: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PHE A 905 " pdb=" N PHE A 905 " pdb=" C PHE A 905 " pdb=" CB PHE A 905 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" C3' DG P 20 " pdb=" C4' DG P 20 " pdb=" O3' DG P 20 " pdb=" C2' DG P 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" C3' DC T 19 " pdb=" C4' DC T 19 " pdb=" O3' DC T 19 " pdb=" C2' DC T 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1479 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " -0.035 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP A 40 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " 0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 639 " -0.264 9.50e-02 1.11e+02 1.19e-01 1.05e+01 pdb=" NE ARG A 639 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 639 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 639 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.240 9.50e-02 1.11e+02 1.08e-01 8.93e+00 pdb=" NE ARG A 346 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.001 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 558 2.73 - 3.27: 9508 3.27 - 3.82: 14614 3.82 - 4.36: 18295 4.36 - 4.90: 31515 Nonbonded interactions: 74490 Sorted by model distance: nonbonded pdb=" OD2 ASP A 862 " pdb="CA CA A1303 " model vdw 2.191 2.510 nonbonded pdb=" O VAL A 627 " pdb="CA CA A1303 " model vdw 2.209 2.510 nonbonded pdb=" O1A DDS A1302 " pdb="CA CA A1303 " model vdw 2.214 2.510 nonbonded pdb=" NH1 ARG A 310 " pdb=" OD1 ASP A 316 " model vdw 2.236 3.120 nonbonded pdb=" NZ LYS A 526 " pdb=" OE1 GLU A 537 " model vdw 2.319 3.120 ... (remaining 74485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.004 0.126 10080 Z= 0.266 Angle : 0.756 15.044 13774 Z= 0.487 Chirality : 0.046 0.193 1482 Planarity : 0.010 0.119 1660 Dihedral : 17.197 157.589 3914 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1114 helix: -1.38 (0.20), residues: 461 sheet: 0.17 (0.34), residues: 210 loop : -0.38 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.004 ARG A 639 TYR 0.026 0.005 TYR A 816 PHE 0.029 0.004 PHE A 905 TRP 0.045 0.008 TRP A 40 HIS 0.006 0.002 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.26 (10076) covalent geometry : angle 0.72406 / 0.49 (13762) hydrogen bonds : bond 0.15349 / 10.54 ( 473) hydrogen bonds : angle 6.74979 / 4.84 ( 1318) metal coordination : bond 0.05581 / 2.81 ( 4) metal coordination : angle 7.36125 / 4.28 ( 12) *********************** 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 192 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8338 (pt) cc_final: 0.8105 (pt) REVERT: A 383 MET cc_start: 0.7591 (ttp) cc_final: 0.7249 (ttp) REVERT: A 444 MET cc_start: 0.8054 (mtm) cc_final: 0.7765 (mtm) REVERT: A 506 MET cc_start: 0.8857 (mtm) cc_final: 0.8526 (mtm) REVERT: A 631 TYR cc_start: 0.8732 (m-10) cc_final: 0.8515 (m-10) REVERT: A 876 PHE cc_start: 0.7669 (m-80) cc_final: 0.7403 (m-80) REVERT: A 1024 MET cc_start: 0.6856 (ttm) cc_final: 0.6652 (mtp) REVERT: A 1037 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.6931 (mtp180) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1356 time to fit residues: 33.9446 Evaluate side-chains 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 404 HIS A 475 HIS A 511 HIS A 543 HIS A 592 GLN A 687 GLN A 808 HIS A 980 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111494 restraints weight = 13619.780| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.18 r_work: 0.3139 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10080 Z= 0.175 Angle : 0.687 16.122 13774 Z= 0.366 Chirality : 0.044 0.180 1482 Planarity : 0.005 0.050 1660 Dihedral : 17.285 142.390 1604 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.21 % Allowed : 8.59 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1114 helix: 0.31 (0.23), residues: 482 sheet: 0.33 (0.35), residues: 201 loop : -0.06 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.012 0.002 TYR A1132 PHE 0.017 0.002 PHE A 872 TRP 0.016 0.002 TRP A 40 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (10076) covalent geometry : angle 0.65429 / 0.37 (13762) hydrogen bonds : bond 0.06289 / 4.21 ( 473) hydrogen bonds : angle 5.12390 / 3.66 ( 1318) metal coordination : bond 0.01348 / 0.69 ( 4) metal coordination : angle 7.12023 / 4.02 ( 12) *********************** 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 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8345 (tt0) cc_final: 0.7403 (pm20) REVERT: A 383 MET cc_start: 0.8288 (ttp) cc_final: 0.7893 (ttp) REVERT: A 444 MET cc_start: 0.8658 (mtm) cc_final: 0.8299 (mtm) REVERT: A 506 MET cc_start: 0.9236 (mtm) cc_final: 0.9035 (mtm) REVERT: A 1037 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7720 (mtp180) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.1063 time to fit residues: 17.0996 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 890 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 592 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109558 restraints weight = 13626.398| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.16 r_work: 0.3154 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10080 Z= 0.178 Angle : 0.640 15.547 13774 Z= 0.340 Chirality : 0.044 0.160 1482 Planarity : 0.005 0.050 1660 Dihedral : 17.055 145.473 1604 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.31 % Allowed : 11.21 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1114 helix: 0.74 (0.23), residues: 484 sheet: 0.19 (0.34), residues: 205 loop : -0.11 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 413 TYR 0.012 0.002 TYR A 726 PHE 0.018 0.002 PHE A 753 TRP 0.011 0.002 TRP A 40 HIS 0.008 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10076) covalent geometry : angle 0.60817 / 0.34 (13762) hydrogen bonds : bond 0.05999 / 4.02 ( 473) hydrogen bonds : angle 4.74881 / 3.38 ( 1318) metal coordination : bond 0.00900 / 0.45 ( 4) metal coordination : angle 6.78463 / 3.80 ( 12) *********************** 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.386 Fit side-chains REVERT: A 51 GLU cc_start: 0.8260 (tt0) cc_final: 0.7463 (pm20) REVERT: A 83 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8522 (m-30) REVERT: A 383 MET cc_start: 0.8254 (ttp) cc_final: 0.7841 (ttp) REVERT: A 444 MET cc_start: 0.8766 (mtm) cc_final: 0.8439 (mtm) REVERT: A 506 MET cc_start: 0.9239 (mtm) cc_final: 0.8979 (mtm) REVERT: A 775 TRP cc_start: 0.7374 (m100) cc_final: 0.6864 (m100) REVERT: A 1023 ASN cc_start: 0.8035 (t0) cc_final: 0.7723 (t0) REVERT: A 1037 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7882 (ttm110) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.1106 time to fit residues: 16.7373 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1019 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 592 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112095 restraints weight = 13767.770| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.16 r_work: 0.3195 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10080 Z= 0.123 Angle : 0.568 13.487 13774 Z= 0.301 Chirality : 0.041 0.136 1482 Planarity : 0.004 0.047 1660 Dihedral : 16.695 156.507 1604 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.31 % Allowed : 12.32 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1114 helix: 1.21 (0.24), residues: 488 sheet: 0.32 (0.34), residues: 206 loop : 0.00 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 793 TYR 0.011 0.001 TYR A 248 PHE 0.014 0.001 PHE A 876 TRP 0.009 0.001 TRP A 669 HIS 0.010 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (10076) covalent geometry : angle 0.54047 / 0.30 (13762) hydrogen bonds : bond 0.04782 / 3.19 ( 473) hydrogen bonds : angle 4.40158 / 3.13 ( 1318) metal coordination : bond 0.00450 / 0.23 ( 4) metal coordination : angle 5.99363 / 3.30 ( 12) *********************** 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 119 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.280 Fit side-chains REVERT: A 51 GLU cc_start: 0.8303 (tt0) cc_final: 0.7578 (pm20) REVERT: A 383 MET cc_start: 0.8192 (ttp) cc_final: 0.7749 (ttp) REVERT: A 444 MET cc_start: 0.8751 (mtm) cc_final: 0.8413 (mtm) REVERT: A 506 MET cc_start: 0.9180 (mtm) cc_final: 0.8891 (mtm) REVERT: A 684 HIS cc_start: 0.6160 (OUTLIER) cc_final: 0.5953 (t-90) REVERT: A 775 TRP cc_start: 0.7366 (m100) cc_final: 0.6890 (m100) REVERT: A 1023 ASN cc_start: 0.7876 (t0) cc_final: 0.7551 (t0) REVERT: A 1037 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7879 (ttm110) outliers start: 13 outliers final: 10 residues processed: 113 average time/residue: 0.1076 time to fit residues: 17.0647 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1055 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113369 restraints weight = 13508.688| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.04 r_work: 0.3205 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10080 Z= 0.174 Angle : 0.606 14.256 13774 Z= 0.322 Chirality : 0.043 0.143 1482 Planarity : 0.005 0.050 1660 Dihedral : 16.616 167.762 1604 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.63 % Allowed : 12.53 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1114 helix: 1.16 (0.24), residues: 489 sheet: 0.12 (0.35), residues: 203 loop : -0.01 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.013 0.002 TYR A 683 PHE 0.017 0.002 PHE A 753 TRP 0.009 0.002 TRP A 369 HIS 0.009 0.001 HIS A 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (10076) covalent geometry : angle 0.57717 / 0.32 (13762) hydrogen bonds : bond 0.05450 / 3.66 ( 473) hydrogen bonds : angle 4.41301 / 3.15 ( 1318) metal coordination : bond 0.00826 / 0.41 ( 4) metal coordination : angle 6.28720 / 3.49 ( 12) *********************** 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 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.322 Fit side-chains REVERT: A 51 GLU cc_start: 0.8373 (tt0) cc_final: 0.7726 (pm20) REVERT: A 58 GLU cc_start: 0.7565 (tt0) cc_final: 0.7045 (tt0) REVERT: A 83 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: A 383 MET cc_start: 0.8237 (ttp) cc_final: 0.7817 (ttp) REVERT: A 444 MET cc_start: 0.8714 (mtm) cc_final: 0.8349 (mtm) REVERT: A 506 MET cc_start: 0.9174 (mtm) cc_final: 0.8813 (mtm) REVERT: A 684 HIS cc_start: 0.6116 (OUTLIER) cc_final: 0.5830 (t70) REVERT: A 775 TRP cc_start: 0.7463 (m100) cc_final: 0.7004 (m100) REVERT: A 776 LYS cc_start: 0.7524 (ttpt) cc_final: 0.7232 (ttpt) REVERT: A 1023 ASN cc_start: 0.7776 (t0) cc_final: 0.7447 (t0) REVERT: A 1037 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7921 (ttm110) outliers start: 26 outliers final: 17 residues processed: 105 average time/residue: 0.1074 time to fit residues: 15.9287 Evaluate side-chains 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116438 restraints weight = 13472.871| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.03 r_work: 0.3248 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10080 Z= 0.113 Angle : 0.544 12.514 13774 Z= 0.289 Chirality : 0.040 0.132 1482 Planarity : 0.004 0.051 1660 Dihedral : 16.309 175.839 1604 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.02 % Allowed : 13.43 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1114 helix: 1.47 (0.24), residues: 485 sheet: 0.34 (0.36), residues: 201 loop : 0.00 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.010 0.001 TYR A 248 PHE 0.015 0.001 PHE A 366 TRP 0.008 0.001 TRP A 410 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (10076) covalent geometry : angle 0.51864 / 0.29 (13762) hydrogen bonds : bond 0.04530 / 3.04 ( 473) hydrogen bonds : angle 4.18918 / 2.98 ( 1318) metal coordination : bond 0.00448 / 0.23 ( 4) metal coordination : angle 5.60778 / 3.08 ( 12) *********************** 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 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.365 Fit side-chains REVERT: A 51 GLU cc_start: 0.8312 (tt0) cc_final: 0.7676 (pm20) REVERT: A 383 MET cc_start: 0.8183 (ttp) cc_final: 0.7749 (ttp) REVERT: A 506 MET cc_start: 0.9123 (mtm) cc_final: 0.8693 (mtm) REVERT: A 525 ASN cc_start: 0.7499 (m-40) cc_final: 0.6582 (p0) REVERT: A 775 TRP cc_start: 0.7425 (m100) cc_final: 0.7130 (m100) REVERT: A 776 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7230 (ttpt) REVERT: A 1023 ASN cc_start: 0.7666 (t0) cc_final: 0.7327 (t0) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.1120 time to fit residues: 17.1175 Evaluate side-chains 104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115394 restraints weight = 13538.929| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.04 r_work: 0.3232 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10080 Z= 0.129 Angle : 0.554 12.426 13774 Z= 0.294 Chirality : 0.040 0.137 1482 Planarity : 0.004 0.053 1660 Dihedral : 16.051 161.610 1604 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.22 % Allowed : 13.23 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1114 helix: 1.54 (0.24), residues: 485 sheet: 0.35 (0.36), residues: 202 loop : -0.05 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1037 TYR 0.017 0.001 TYR A1133 PHE 0.014 0.001 PHE A 104 TRP 0.008 0.001 TRP A 369 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10076) covalent geometry : angle 0.52818 / 0.29 (13762) hydrogen bonds : bond 0.04674 / 3.14 ( 473) hydrogen bonds : angle 4.15072 / 2.95 ( 1318) metal coordination : bond 0.00543 / 0.27 ( 4) metal coordination : angle 5.65696 / 3.11 ( 12) *********************** 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 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.344 Fit side-chains REVERT: A 51 GLU cc_start: 0.8410 (tt0) cc_final: 0.7738 (pm20) REVERT: A 383 MET cc_start: 0.8195 (ttp) cc_final: 0.7759 (ttp) REVERT: A 712 ARG cc_start: 0.4425 (tpt170) cc_final: 0.3912 (tpt-90) REVERT: A 775 TRP cc_start: 0.7392 (m100) cc_final: 0.7100 (m100) REVERT: A 776 LYS cc_start: 0.7485 (ttpt) cc_final: 0.7211 (ttpt) REVERT: A 1023 ASN cc_start: 0.7670 (t0) cc_final: 0.7346 (t0) REVERT: A 1037 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7479 (mtp180) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.1096 time to fit residues: 16.0561 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115245 restraints weight = 13630.449| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.13 r_work: 0.3240 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10080 Z= 0.116 Angle : 0.548 13.242 13774 Z= 0.289 Chirality : 0.040 0.131 1482 Planarity : 0.004 0.053 1660 Dihedral : 15.896 150.084 1604 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.12 % Allowed : 13.43 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1114 helix: 1.64 (0.24), residues: 486 sheet: 0.32 (0.36), residues: 207 loop : -0.01 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1037 TYR 0.014 0.001 TYR A1133 PHE 0.014 0.001 PHE A 104 TRP 0.008 0.001 TRP A 369 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (10076) covalent geometry : angle 0.52485 / 0.29 (13762) hydrogen bonds : bond 0.04370 / 2.93 ( 473) hydrogen bonds : angle 4.08892 / 2.91 ( 1318) metal coordination : bond 0.00472 / 0.24 ( 4) metal coordination : angle 5.38288 / 2.95 ( 12) *********************** 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 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.384 Fit side-chains REVERT: A 51 GLU cc_start: 0.8396 (tt0) cc_final: 0.7713 (pm20) REVERT: A 83 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8273 (m-30) REVERT: A 383 MET cc_start: 0.8201 (ttp) cc_final: 0.7744 (ttp) REVERT: A 776 LYS cc_start: 0.7400 (ttpt) cc_final: 0.7185 (ttpt) REVERT: A 940 MET cc_start: 0.8323 (tpp) cc_final: 0.7868 (ttt) REVERT: A 1023 ASN cc_start: 0.7706 (t0) cc_final: 0.7390 (t0) REVERT: A 1037 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7451 (mtp180) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 0.1122 time to fit residues: 16.8311 Evaluate side-chains 100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115315 restraints weight = 13560.559| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.13 r_work: 0.3242 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10080 Z= 0.117 Angle : 0.540 11.360 13774 Z= 0.286 Chirality : 0.040 0.133 1482 Planarity : 0.004 0.055 1660 Dihedral : 15.778 144.246 1604 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1114 helix: 1.71 (0.24), residues: 486 sheet: 0.34 (0.36), residues: 207 loop : 0.04 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.014 0.001 TYR A1133 PHE 0.014 0.001 PHE A 104 TRP 0.007 0.001 TRP A 369 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10076) covalent geometry : angle 0.51723 / 0.29 (13762) hydrogen bonds : bond 0.04287 / 2.88 ( 473) hydrogen bonds : angle 4.04883 / 2.88 ( 1318) metal coordination : bond 0.00461 / 0.23 ( 4) metal coordination : angle 5.29395 / 2.90 ( 12) *********************** 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 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.363 Fit side-chains REVERT: A 51 GLU cc_start: 0.8366 (tt0) cc_final: 0.7727 (pm20) REVERT: A 83 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: A 168 LYS cc_start: 0.8059 (mttt) cc_final: 0.7844 (mttp) REVERT: A 231 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8478 (tpp-160) REVERT: A 232 LEU cc_start: 0.8914 (tp) cc_final: 0.8687 (tp) REVERT: A 383 MET cc_start: 0.8210 (ttp) cc_final: 0.7748 (ttp) REVERT: A 776 LYS cc_start: 0.7367 (ttpt) cc_final: 0.7153 (ttpt) REVERT: A 940 MET cc_start: 0.8435 (tpp) cc_final: 0.8050 (ttt) REVERT: A 1023 ASN cc_start: 0.7726 (t0) cc_final: 0.7415 (t0) REVERT: A 1037 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7400 (mtp180) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.1178 time to fit residues: 16.6467 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115458 restraints weight = 13568.045| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.13 r_work: 0.3243 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10080 Z= 0.116 Angle : 0.545 14.717 13774 Z= 0.286 Chirality : 0.040 0.130 1482 Planarity : 0.004 0.055 1660 Dihedral : 15.671 138.132 1604 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.82 % Allowed : 14.04 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1114 helix: 1.76 (0.24), residues: 486 sheet: 0.35 (0.36), residues: 208 loop : 0.09 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.012 0.001 TYR A1133 PHE 0.014 0.001 PHE A 104 TRP 0.008 0.001 TRP A 40 HIS 0.008 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10076) covalent geometry : angle 0.52251 / 0.29 (13762) hydrogen bonds : bond 0.04251 / 2.86 ( 473) hydrogen bonds : angle 4.00856 / 2.85 ( 1318) metal coordination : bond 0.00460 / 0.23 ( 4) metal coordination : angle 5.33370 / 2.92 ( 12) ********************** 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 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.320 Fit side-chains REVERT: A 51 GLU cc_start: 0.8370 (tt0) cc_final: 0.7733 (pm20) REVERT: A 83 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: A 168 LYS cc_start: 0.8075 (mttt) cc_final: 0.7858 (mttp) REVERT: A 231 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8461 (tpp-160) REVERT: A 232 LEU cc_start: 0.8908 (tp) cc_final: 0.8676 (tp) REVERT: A 383 MET cc_start: 0.8209 (ttp) cc_final: 0.7746 (ttp) REVERT: A 776 LYS cc_start: 0.7299 (ttpt) cc_final: 0.7073 (ttpt) REVERT: A 940 MET cc_start: 0.8409 (tpp) cc_final: 0.8099 (ttt) REVERT: A 1023 ASN cc_start: 0.7726 (t0) cc_final: 0.7421 (t0) REVERT: A 1037 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7435 (mtp180) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.1215 time to fit residues: 17.3231 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115951 restraints weight = 13397.793| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.08 r_work: 0.3240 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10080 Z= 0.119 Angle : 0.541 11.600 13774 Z= 0.286 Chirality : 0.040 0.138 1482 Planarity : 0.004 0.056 1660 Dihedral : 15.622 135.174 1604 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.82 % Allowed : 14.24 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1114 helix: 1.76 (0.24), residues: 486 sheet: 0.35 (0.36), residues: 206 loop : 0.10 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.013 0.001 TYR A 224 PHE 0.017 0.001 PHE A1030 TRP 0.007 0.001 TRP A 369 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10076) covalent geometry : angle 0.51710 / 0.29 (13762) hydrogen bonds : bond 0.04303 / 2.88 ( 473) hydrogen bonds : angle 4.00638 / 2.85 ( 1318) metal coordination : bond 0.00495 / 0.25 ( 4) metal coordination : angle 5.38042 / 2.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.65 seconds wall clock time: 45 minutes 27.23 seconds (2727.23 seconds total)