Starting phenix.real_space_refine on Thu Jul 2 19:00:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6i_50225/07_2026/9f6i_50225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6i_50225/07_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_50225/07_2026/9f6i_50225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6i_50225/07_2026/9f6i_50225.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6i_50225/07_2026/9f6i_50225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6i_50225/07_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-dev-6108/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, 37 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DDS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 1.96, per 1000 atoms: 0.20 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: 0.87 Conformation dependent library (CDL) restraints added in 208.7 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: 1.97 Time building geometry restraints manager: 1.10 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: 12745 1.26 - 2.52: 831 2.52 - 3.78: 152 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 3.250 nonbonded pdb=" O VAL A 627 " pdb="CA CA A1303 " model vdw 2.209 3.250 nonbonded pdb=" O1A DDS A1302 " pdb="CA CA A1303 " model vdw 2.214 3.250 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: 1.200 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- 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 : 0.753 15.044 13774 Z= 0.483 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 0.72172 / 0.48 (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 : 0.381 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: 0.7250 (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: 0.8527 (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: 0.1138 time to fit residues: 28.4945 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 : 0.343 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.145955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111619 restraints weight = 13639.225| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.13 r_work: 0.3184 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10080 Z= 0.179 Angle : 0.701 16.465 13774 Z= 0.371 Chirality : 0.045 0.161 1482 Planarity : 0.005 0.050 1660 Dihedral : 17.363 146.516 1604 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.21 % Allowed : 9.19 % Favored : 89.60 % 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: 0.33 (0.23), residues: 482 sheet: 0.31 (0.34), residues: 201 loop : -0.07 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.014 0.002 TYR A1132 PHE 0.019 0.002 PHE A 872 TRP 0.015 0.002 TRP A 40 HIS 0.005 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (10076) covalent geometry : angle 0.66874 / 0.37 (13762) hydrogen bonds : bond 0.06172 / 4.13 ( 473) hydrogen bonds : angle 5.04452 / 3.60 ( 1318) metal coordination : bond 0.01227 / 0.63 ( 4) metal coordination : angle 7.13389 / 4.01 ( 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 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.328 Fit side-chains REVERT: A 51 GLU cc_start: 0.8356 (tt0) cc_final: 0.7471 (pm20) REVERT: A 383 MET cc_start: 0.8282 (ttp) cc_final: 0.7877 (ttp) REVERT: A 444 MET cc_start: 0.8782 (mtm) cc_final: 0.8417 (mtm) REVERT: A 1037 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7918 (ttm110) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.0848 time to fit residues: 13.6947 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 601 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1019 SER 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: 0.9990 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3694 r_free = 0.3694 target = 0.143423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108993 restraints weight = 13649.498| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.12 r_work: 0.3157 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10080 Z= 0.184 Angle : 0.641 15.323 13774 Z= 0.343 Chirality : 0.044 0.151 1482 Planarity : 0.005 0.049 1660 Dihedral : 17.090 145.306 1604 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.92 % Allowed : 11.21 % Favored : 86.87 % 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: 0.39 (0.25), residues: 1114 helix: 0.78 (0.23), residues: 483 sheet: 0.13 (0.34), residues: 209 loop : -0.10 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 825 TYR 0.012 0.002 TYR A 827 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 0.00413 / 0.18 (10076) covalent geometry : angle 0.61048 / 0.34 (13762) hydrogen bonds : bond 0.06054 / 4.06 ( 473) hydrogen bonds : angle 4.70910 / 3.35 ( 1318) metal coordination : bond 0.00877 / 0.44 ( 4) metal coordination : angle 6.70447 / 3.76 ( 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 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.381 Fit side-chains REVERT: A 51 GLU cc_start: 0.8255 (tt0) cc_final: 0.7467 (pm20) REVERT: A 83 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8428 (m-30) REVERT: A 383 MET cc_start: 0.8295 (ttp) cc_final: 0.7888 (ttp) REVERT: A 444 MET cc_start: 0.8764 (mtm) cc_final: 0.8434 (mtm) REVERT: A 684 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5937 (t-90) REVERT: A 775 TRP cc_start: 0.7430 (m100) cc_final: 0.6932 (m100) REVERT: A 1023 ASN cc_start: 0.7937 (t0) cc_final: 0.7609 (t0) REVERT: A 1037 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7906 (ttm110) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.0837 time to fit residues: 12.9165 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 460 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3739 r_free = 0.3739 target = 0.146529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112247 restraints weight = 13585.950| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.03 r_work: 0.3191 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10080 Z= 0.183 Angle : 0.638 15.057 13774 Z= 0.337 Chirality : 0.043 0.149 1482 Planarity : 0.005 0.049 1660 Dihedral : 17.009 145.900 1604 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 12.32 % Favored : 85.66 % 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: 0.45 (0.25), residues: 1114 helix: 0.85 (0.23), residues: 488 sheet: 0.10 (0.34), residues: 209 loop : -0.07 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 793 TYR 0.013 0.002 TYR A 827 PHE 0.018 0.002 PHE A 753 TRP 0.010 0.002 TRP A 40 HIS 0.011 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (10076) covalent geometry : angle 0.60678 / 0.34 (13762) hydrogen bonds : bond 0.05930 / 3.96 ( 473) hydrogen bonds : angle 4.61239 / 3.28 ( 1318) metal coordination : bond 0.00854 / 0.43 ( 4) metal coordination : angle 6.69316 / 3.76 ( 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 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.234 Fit side-chains REVERT: A 51 GLU cc_start: 0.8314 (tt0) cc_final: 0.7620 (pm20) REVERT: A 83 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8486 (m-30) REVERT: A 383 MET cc_start: 0.8243 (ttp) cc_final: 0.7846 (ttp) REVERT: A 444 MET cc_start: 0.8721 (mtm) cc_final: 0.8408 (mtm) REVERT: A 775 TRP cc_start: 0.7385 (m100) cc_final: 0.6942 (m100) REVERT: A 1023 ASN cc_start: 0.7894 (t0) cc_final: 0.7582 (t0) REVERT: A 1037 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7922 (ttm110) outliers start: 20 outliers final: 15 residues processed: 108 average time/residue: 0.0799 time to fit residues: 12.2260 Evaluate side-chains 109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 290 THR 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 676 MET 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 1045 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114628 restraints weight = 13597.400| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.15 r_work: 0.3232 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 10080 Z= 0.120 Angle : 0.550 12.516 13774 Z= 0.294 Chirality : 0.040 0.139 1482 Planarity : 0.004 0.044 1660 Dihedral : 16.751 148.091 1604 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.92 % Allowed : 13.03 % Favored : 85.05 % 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: 0.87 (0.25), residues: 1114 helix: 1.28 (0.24), residues: 488 sheet: 0.35 (0.35), residues: 206 loop : -0.01 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.010 0.001 TYR A 468 PHE 0.014 0.001 PHE A 104 TRP 0.009 0.001 TRP A 410 HIS 0.010 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10076) covalent geometry : angle 0.52444 / 0.29 (13762) hydrogen bonds : bond 0.04690 / 3.14 ( 473) hydrogen bonds : angle 4.29055 / 3.05 ( 1318) metal coordination : bond 0.00466 / 0.24 ( 4) metal coordination : angle 5.68815 / 3.14 ( 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: 19 poor density : 98 time to evaluate : 0.227 Fit side-chains REVERT: A 51 GLU cc_start: 0.8348 (tt0) cc_final: 0.7675 (pm20) REVERT: A 58 GLU cc_start: 0.7651 (tt0) cc_final: 0.7098 (tt0) REVERT: A 247 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.8149 (mmm-85) REVERT: A 383 MET cc_start: 0.8208 (ttp) cc_final: 0.7801 (ttp) REVERT: A 444 MET cc_start: 0.8708 (mtm) cc_final: 0.8381 (mtm) REVERT: A 775 TRP cc_start: 0.7448 (m100) cc_final: 0.7018 (m100) REVERT: A 776 LYS cc_start: 0.7526 (ttpt) cc_final: 0.7230 (ttpt) REVERT: A 932 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: A 1023 ASN cc_start: 0.7853 (t0) cc_final: 0.7548 (t0) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.0790 time to fit residues: 12.0835 Evaluate side-chains 100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 460 VAL 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 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3777 r_free = 0.3777 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115804 restraints weight = 13524.335| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.06 r_work: 0.3236 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10080 Z= 0.121 Angle : 0.555 12.954 13774 Z= 0.293 Chirality : 0.040 0.135 1482 Planarity : 0.004 0.051 1660 Dihedral : 16.632 149.949 1604 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.92 % Allowed : 13.54 % 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: 0.98 (0.25), residues: 1114 helix: 1.45 (0.24), residues: 488 sheet: 0.36 (0.35), residues: 209 loop : -0.02 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1037 TYR 0.010 0.001 TYR A1132 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 0.00246 / 0.12 (10076) covalent geometry : angle 0.53075 / 0.29 (13762) hydrogen bonds : bond 0.04627 / 3.11 ( 473) hydrogen bonds : angle 4.16885 / 2.97 ( 1318) metal coordination : bond 0.00473 / 0.24 ( 4) metal coordination : angle 5.53174 / 3.04 ( 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 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.248 Fit side-chains REVERT: A 51 GLU cc_start: 0.8312 (tt0) cc_final: 0.7681 (pm20) REVERT: A 58 GLU cc_start: 0.7852 (tt0) cc_final: 0.7250 (tt0) REVERT: A 168 LYS cc_start: 0.8051 (mttt) cc_final: 0.7828 (mttp) REVERT: A 247 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.8153 (mmm-85) REVERT: A 383 MET cc_start: 0.8206 (ttp) cc_final: 0.7785 (ttp) REVERT: A 444 MET cc_start: 0.8640 (mtm) cc_final: 0.8288 (mtm) REVERT: A 775 TRP cc_start: 0.7419 (m100) cc_final: 0.7132 (m100) REVERT: A 776 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7202 (ttpt) REVERT: A 932 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: A 940 MET cc_start: 0.8351 (tpp) cc_final: 0.7797 (ttt) REVERT: A 1023 ASN cc_start: 0.7779 (t0) cc_final: 0.7476 (t0) REVERT: A 1037 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7469 (mtp180) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.0911 time to fit residues: 13.0063 Evaluate side-chains 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 361 THR Chi-restraints excluded: chain A residue 460 VAL 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 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: 0.9990 chunk 33 optimal weight: 0.0270 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 chunk 61 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.151252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117177 restraints weight = 13518.536| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.09 r_work: 0.3260 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10080 Z= 0.106 Angle : 0.521 10.887 13774 Z= 0.277 Chirality : 0.039 0.129 1482 Planarity : 0.004 0.052 1660 Dihedral : 16.490 150.395 1604 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.92 % Allowed : 14.04 % Favored : 84.04 % 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: 1.19 (0.25), residues: 1114 helix: 1.71 (0.24), residues: 485 sheet: 0.38 (0.36), residues: 205 loop : 0.03 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1037 TYR 0.015 0.001 TYR A1133 PHE 0.013 0.001 PHE A 104 TRP 0.009 0.001 TRP A 775 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 (10076) covalent geometry : angle 0.49957 / 0.28 (13762) hydrogen bonds : bond 0.04016 / 2.69 ( 473) hydrogen bonds : angle 4.02563 / 2.86 ( 1318) metal coordination : bond 0.00441 / 0.23 ( 4) metal coordination : angle 5.06858 / 2.75 ( 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 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.348 Fit side-chains REVERT: A 51 GLU cc_start: 0.8387 (tt0) cc_final: 0.7700 (pm20) REVERT: A 58 GLU cc_start: 0.7645 (tt0) cc_final: 0.7164 (tt0) REVERT: A 168 LYS cc_start: 0.8009 (mttt) cc_final: 0.7798 (mttp) REVERT: A 231 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8463 (tpp-160) REVERT: A 383 MET cc_start: 0.8183 (ttp) cc_final: 0.7749 (ttp) REVERT: A 444 MET cc_start: 0.8581 (mtm) cc_final: 0.8376 (mtm) REVERT: A 776 LYS cc_start: 0.7387 (ttpt) cc_final: 0.7160 (ttpt) REVERT: A 932 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: A 940 MET cc_start: 0.8441 (tpp) cc_final: 0.7965 (ttt) REVERT: A 1023 ASN cc_start: 0.7704 (t0) cc_final: 0.7402 (t0) REVERT: A 1037 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7449 (mtp180) outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 0.0941 time to fit residues: 14.4606 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 460 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.150961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116626 restraints weight = 13496.472| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.05 r_work: 0.3250 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10080 Z= 0.121 Angle : 0.547 12.469 13774 Z= 0.288 Chirality : 0.040 0.132 1482 Planarity : 0.004 0.054 1660 Dihedral : 16.475 151.187 1604 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % 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: 1.17 (0.25), residues: 1114 helix: 1.71 (0.24), residues: 486 sheet: 0.40 (0.36), residues: 205 loop : -0.02 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 247 TYR 0.020 0.001 TYR A1133 PHE 0.015 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 0.00255 / 0.12 (10076) covalent geometry : angle 0.52465 / 0.29 (13762) hydrogen bonds : bond 0.04302 / 2.89 ( 473) hydrogen bonds : angle 4.01306 / 2.86 ( 1318) metal coordination : bond 0.00491 / 0.25 ( 4) metal coordination : angle 5.23813 / 2.87 ( 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 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.364 Fit side-chains REVERT: A 51 GLU cc_start: 0.8363 (tt0) cc_final: 0.7750 (pm20) REVERT: A 83 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: A 168 LYS cc_start: 0.8039 (mttt) cc_final: 0.7825 (mttp) REVERT: A 231 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8500 (tpp-160) REVERT: A 247 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: A 383 MET cc_start: 0.8125 (ttp) cc_final: 0.7665 (ttp) REVERT: A 776 LYS cc_start: 0.7379 (ttpt) cc_final: 0.7159 (ttpt) REVERT: A 940 MET cc_start: 0.8460 (tpp) cc_final: 0.8024 (ttt) REVERT: A 1023 ASN cc_start: 0.7685 (t0) cc_final: 0.7390 (t0) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.0914 time to fit residues: 13.2657 Evaluate side-chains 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 888 VAL 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: 0.7980 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 102 optimal weight: 0.0050 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7008 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.149743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115710 restraints weight = 13370.241| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.05 r_work: 0.3250 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10080 Z= 0.115 Angle : 0.536 11.202 13774 Z= 0.283 Chirality : 0.039 0.130 1482 Planarity : 0.004 0.054 1660 Dihedral : 16.437 152.396 1604 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % 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: 1.25 (0.25), residues: 1114 helix: 1.79 (0.24), residues: 486 sheet: 0.44 (0.36), residues: 205 loop : -0.00 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1037 TYR 0.021 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 0.00236 / 0.11 (10076) covalent geometry : angle 0.51311 / 0.28 (13762) hydrogen bonds : bond 0.04180 / 2.81 ( 473) hydrogen bonds : angle 3.98218 / 2.83 ( 1318) metal coordination : bond 0.00446 / 0.23 ( 4) metal coordination : angle 5.22979 / 2.87 ( 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 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.230 Fit side-chains REVERT: A 51 GLU cc_start: 0.8363 (tt0) cc_final: 0.7736 (pm20) REVERT: A 83 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: A 168 LYS cc_start: 0.8040 (mttt) cc_final: 0.7829 (mttp) REVERT: A 216 ASP cc_start: 0.7605 (p0) cc_final: 0.7391 (p0) REVERT: A 231 ARG cc_start: 0.8727 (tpp-160) cc_final: 0.8496 (tpp-160) REVERT: A 247 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7727 (mmm-85) REVERT: A 383 MET cc_start: 0.8127 (ttp) cc_final: 0.7671 (ttp) REVERT: A 926 GLU cc_start: 0.7361 (tt0) cc_final: 0.7023 (tt0) REVERT: A 940 MET cc_start: 0.8409 (tpp) cc_final: 0.7981 (ttt) REVERT: A 1023 ASN cc_start: 0.7710 (t0) cc_final: 0.7230 (t0) REVERT: A 1037 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7321 (mtp180) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.1023 time to fit residues: 14.7511 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain A residue 888 VAL 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 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: 0.5980 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.149841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115317 restraints weight = 13553.841| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.09 r_work: 0.3243 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3582 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= 0.124 Angle : 0.553 13.365 13774 Z= 0.290 Chirality : 0.040 0.132 1482 Planarity : 0.004 0.057 1660 Dihedral : 16.431 154.697 1604 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % 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: 1.22 (0.25), residues: 1114 helix: 1.78 (0.24), residues: 486 sheet: 0.37 (0.36), residues: 208 loop : -0.00 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1037 TYR 0.020 0.001 TYR A1133 PHE 0.015 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 0.00266 / 0.12 (10076) covalent geometry : angle 0.53022 / 0.29 (13762) hydrogen bonds : bond 0.04371 / 2.93 ( 473) hydrogen bonds : angle 3.99957 / 2.84 ( 1318) metal coordination : bond 0.00479 / 0.24 ( 4) metal coordination : angle 5.38183 / 2.96 ( 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 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.261 Fit side-chains REVERT: A 39 GLN cc_start: 0.7853 (mp10) cc_final: 0.7650 (mp10) REVERT: A 51 GLU cc_start: 0.8386 (tt0) cc_final: 0.7752 (pm20) REVERT: A 83 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: A 168 LYS cc_start: 0.8075 (mttt) cc_final: 0.7862 (mttp) REVERT: A 216 ASP cc_start: 0.7488 (p0) cc_final: 0.7265 (p0) REVERT: A 231 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8488 (tpp-160) REVERT: A 247 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7750 (mmm-85) REVERT: A 383 MET cc_start: 0.8122 (ttp) cc_final: 0.7637 (ttp) REVERT: A 940 MET cc_start: 0.8432 (tpp) cc_final: 0.8028 (ttt) REVERT: A 1023 ASN cc_start: 0.7684 (t0) cc_final: 0.7213 (t0) REVERT: A 1037 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7357 (mtp180) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.0842 time to fit residues: 11.6161 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1019 SER 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: 2.9990 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 96 optimal weight: 0.0020 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115467 restraints weight = 13571.604| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.15 r_work: 0.3240 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3644 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 : 0.535 11.233 13774 Z= 0.284 Chirality : 0.040 0.131 1482 Planarity : 0.004 0.055 1660 Dihedral : 16.398 157.790 1604 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 1.28 (0.25), residues: 1114 helix: 1.82 (0.24), residues: 486 sheet: 0.39 (0.37), residues: 206 loop : 0.05 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1037 TYR 0.020 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 0.00237 / 0.12 (10076) covalent geometry : angle 0.51179 / 0.28 (13762) hydrogen bonds : bond 0.04201 / 2.82 ( 473) hydrogen bonds : angle 3.97947 / 2.83 ( 1318) metal coordination : bond 0.00459 / 0.23 ( 4) metal coordination : angle 5.26646 / 2.89 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.44 seconds wall clock time: 34 minutes 40.90 seconds (2080.90 seconds total)