Starting phenix.real_space_refine on Sun Jun 8 11:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.map" model { file = "/net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qks_14050/06_2025/7qks_14050.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 6011 2.51 5 N 1541 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9300 Classifications: {'peptide': 1199} Link IDs: {'PTRANS': 27, 'TRANS': 1171} Chain breaks: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.61 Number of scatterers: 9339 At special positions: 0 Unit cell: (132.246, 105.462, 102.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1740 8.00 N 1541 7.00 C 6011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 72.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 58 through 59 No H-bonds generated for 'chain 'A' and resid 58 through 59' Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.588A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 4.000A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 159 removed outlier: 3.592A pdb=" N HIS A 158 " --> pdb=" O TRP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.555A pdb=" N ILE A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 212 removed outlier: 3.676A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 261 removed outlier: 3.756A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.682A pdb=" N PHE A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 326 removed outlier: 3.648A pdb=" N LYS A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 345 through 372 removed outlier: 3.628A pdb=" N ALA A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 442 removed outlier: 4.406A pdb=" N ILE A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 528 through 532 removed outlier: 4.169A pdb=" N ASP A 531 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 removed outlier: 4.406A pdb=" N SER A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 588 removed outlier: 4.226A pdb=" N GLY A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.053A pdb=" N GLN A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 698 through 706 removed outlier: 3.730A pdb=" N LEU A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 741 Proline residue: A 715 - end of helix removed outlier: 4.065A pdb=" N PHE A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix removed outlier: 4.132A pdb=" N LEU A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 802 removed outlier: 3.664A pdb=" N PHE A 762 " --> pdb=" O LYS A 758 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.840A pdb=" N PHE A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 809 " --> pdb=" O MET A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 809' Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 829 Proline residue: A 826 - end of helix Processing helix chain 'A' and resid 830 through 833 Processing helix chain 'A' and resid 834 through 858 Processing helix chain 'A' and resid 858 through 894 removed outlier: 4.125A pdb=" N VAL A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 866 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 869 " --> pdb=" O CYS A 865 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 3.861A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 removed outlier: 4.028A pdb=" N ALA A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 removed outlier: 3.546A pdb=" N VAL A 911 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 971 removed outlier: 3.615A pdb=" N LYS A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 938 " --> pdb=" O ARG A 934 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 944 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 945 " --> pdb=" O ARG A 941 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 997 Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.649A pdb=" N MET A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1091 removed outlier: 3.876A pdb=" N GLY A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1112 through 1119 Processing helix chain 'A' and resid 1133 through 1139 Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 1153 through 1162 Processing helix chain 'A' and resid 1164 through 1171 Processing helix chain 'A' and resid 1187 through 1202 removed outlier: 4.542A pdb=" N ARG A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1232 removed outlier: 3.764A pdb=" N MET A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 Processing helix chain 'A' and resid 1275 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 418 removed outlier: 6.821A pdb=" N VAL A 410 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG A 401 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER A 412 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 399 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A 414 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 395 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 453 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN A 397 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 451 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.260A pdb=" N ALA A 472 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP A 565 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 474 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 562 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A 595 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 564 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 424 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 423 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL A 609 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A 425 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 611 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 427 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 618 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER A 612 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1067 removed outlier: 6.989A pdb=" N VAL A1059 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG A1050 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A1061 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A1048 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A1063 " --> pdb=" O ASP A1046 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A1047 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A1098 " --> pdb=" O VAL A1047 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 6.466A pdb=" N ALA A1121 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A1210 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1123 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1263 " --> pdb=" O VAL A1255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A1257 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2087 1.33 - 1.45: 1923 1.45 - 1.57: 5412 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9500 Sorted by residual: bond pdb=" N VAL A1076 " pdb=" CA VAL A1076 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.11e-02 8.12e+03 9.76e+00 bond pdb=" C ARG A 405 " pdb=" N PRO A 406 " ideal model delta sigma weight residual 1.334 1.359 -0.026 8.40e-03 1.42e+04 9.45e+00 bond pdb=" N ILE A 346 " pdb=" CA ILE A 346 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" N ILE A 722 " pdb=" CA ILE A 722 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.99e+00 ... (remaining 9495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12308 1.82 - 3.64: 488 3.64 - 5.45: 53 5.45 - 7.27: 6 7.27 - 9.09: 2 Bond angle restraints: 12857 Sorted by residual: angle pdb=" N LYS A 354 " pdb=" CA LYS A 354 " pdb=" C LYS A 354 " ideal model delta sigma weight residual 111.07 106.92 4.15 1.07e+00 8.73e-01 1.50e+01 angle pdb=" N GLY A1174 " pdb=" CA GLY A1174 " pdb=" C GLY A1174 " ideal model delta sigma weight residual 113.18 104.15 9.03 2.37e+00 1.78e-01 1.45e+01 angle pdb=" CA GLY A 170 " pdb=" C GLY A 170 " pdb=" O GLY A 170 " ideal model delta sigma weight residual 120.45 116.61 3.84 1.02e+00 9.61e-01 1.41e+01 angle pdb=" N ASP A 179 " pdb=" CA ASP A 179 " pdb=" C ASP A 179 " ideal model delta sigma weight residual 113.72 109.00 4.72 1.30e+00 5.92e-01 1.32e+01 angle pdb=" N ILE A 523 " pdb=" CA ILE A 523 " pdb=" C ILE A 523 " ideal model delta sigma weight residual 111.45 108.09 3.36 9.30e-01 1.16e+00 1.31e+01 ... (remaining 12852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 5434 24.27 - 48.55: 294 48.55 - 72.82: 31 72.82 - 97.09: 6 97.09 - 121.37: 4 Dihedral angle restraints: 5769 sinusoidal: 2307 harmonic: 3462 Sorted by residual: dihedral pdb=" C21 9Z9 A1301 " pdb=" C22 9Z9 A1301 " pdb=" C23 9Z9 A1301 " pdb=" C24 9Z9 A1301 " ideal model delta sinusoidal sigma weight residual 77.99 -43.38 121.37 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C PHE A 987 " pdb=" N PHE A 987 " pdb=" CA PHE A 987 " pdb=" CB PHE A 987 " ideal model delta harmonic sigma weight residual -122.60 -132.39 9.79 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C18 9Z9 A1301 " pdb=" C17 9Z9 A1301 " pdb=" O20 9Z9 A1301 " pdb=" C21 9Z9 A1301 " ideal model delta sinusoidal sigma weight residual 163.81 -92.29 -103.90 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 5766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1254 0.059 - 0.118: 212 0.118 - 0.177: 31 0.177 - 0.236: 15 0.236 - 0.295: 2 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CA PHE A 987 " pdb=" N PHE A 987 " pdb=" C PHE A 987 " pdb=" CB PHE A 987 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU A1075 " pdb=" N LEU A1075 " pdb=" C LEU A1075 " pdb=" CB LEU A1075 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 706 " pdb=" N ASN A 706 " pdb=" C ASN A 706 " pdb=" CB ASN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1511 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1092 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.06e+00 pdb=" NE ARG A1092 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A1092 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1092 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1092 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 344 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C LEU A 344 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 344 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 345 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 372 " -0.232 9.50e-02 1.11e+02 1.04e-01 6.67e+00 pdb=" NE ARG A 372 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 372 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 372 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 372 " -0.009 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 972 2.75 - 3.29: 9394 3.29 - 3.82: 15174 3.82 - 4.36: 18529 4.36 - 4.90: 32404 Nonbonded interactions: 76473 Sorted by model distance: nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 889 " model vdw 2.210 3.120 nonbonded pdb=" O GLY A 862 " pdb=" OG1 THR A 866 " model vdw 2.221 3.040 nonbonded pdb=" O ILE A1090 " pdb=" OH TYR A1116 " model vdw 2.228 3.040 nonbonded pdb=" O VAL A 939 " pdb=" OG1 THR A 943 " model vdw 2.317 3.040 nonbonded pdb=" O LYS A 909 " pdb=" OG SER A 913 " model vdw 2.346 3.040 ... (remaining 76468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.890 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.005 0.039 9500 Z= 0.343 Angle : 0.738 9.091 12857 Z= 0.506 Chirality : 0.050 0.295 1514 Planarity : 0.007 0.115 1608 Dihedral : 14.589 121.366 3549 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1193 helix: 1.06 (0.18), residues: 779 sheet: -1.59 (0.78), residues: 48 loop : -0.50 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 955 HIS 0.004 0.001 HIS A 103 PHE 0.021 0.001 PHE A 119 TYR 0.025 0.001 TYR A 248 ARG 0.006 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.14880 ( 617) hydrogen bonds : angle 5.78263 ( 1815) covalent geometry : bond 0.00506 ( 9500) covalent geometry : angle 0.73828 (12857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.7896 (m-30) cc_final: 0.7452 (m-30) REVERT: A 1248 GLN cc_start: 0.8532 (tt0) cc_final: 0.8294 (tp40) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2452 time to fit residues: 39.6514 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 637 GLN A1242 HIS A1248 GLN A1267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097213 restraints weight = 11799.055| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.93 r_work: 0.2931 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9500 Z= 0.160 Angle : 0.506 9.585 12857 Z= 0.263 Chirality : 0.039 0.127 1514 Planarity : 0.004 0.054 1608 Dihedral : 6.334 108.945 1395 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.99 % Allowed : 7.42 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1193 helix: 1.51 (0.18), residues: 787 sheet: -1.52 (0.79), residues: 48 loop : -0.25 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.007 0.001 HIS A 103 PHE 0.018 0.002 PHE A1167 TYR 0.024 0.001 TYR A 248 ARG 0.007 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 617) hydrogen bonds : angle 4.34827 ( 1815) covalent geometry : bond 0.00371 ( 9500) covalent geometry : angle 0.50615 (12857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.968 Fit side-chains REVERT: A 165 ASP cc_start: 0.8536 (m-30) cc_final: 0.8117 (m-30) REVERT: A 756 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 1017 ASP cc_start: 0.8413 (t0) cc_final: 0.8158 (t0) REVERT: A 1046 ASP cc_start: 0.8104 (t70) cc_final: 0.7634 (t0) REVERT: A 1050 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6905 (mtp85) REVERT: A 1168 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 1243 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7805 (ptp-170) REVERT: A 1248 GLN cc_start: 0.8859 (tt0) cc_final: 0.8151 (tp40) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2522 time to fit residues: 38.8104 Evaluate side-chains 104 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100144 restraints weight = 11954.189| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.04 r_work: 0.3070 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9500 Z= 0.107 Angle : 0.444 8.072 12857 Z= 0.230 Chirality : 0.037 0.132 1514 Planarity : 0.003 0.045 1608 Dihedral : 5.763 98.678 1391 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.09 % Allowed : 9.59 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1193 helix: 1.93 (0.19), residues: 783 sheet: -1.42 (0.81), residues: 48 loop : -0.18 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.023 0.001 PHE A1167 TYR 0.021 0.001 TYR A 248 ARG 0.003 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 617) hydrogen bonds : angle 4.00570 ( 1815) covalent geometry : bond 0.00222 ( 9500) covalent geometry : angle 0.44396 (12857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.969 Fit side-chains REVERT: A 165 ASP cc_start: 0.8579 (m-30) cc_final: 0.8237 (m-30) REVERT: A 1046 ASP cc_start: 0.8136 (t70) cc_final: 0.7489 (t0) REVERT: A 1054 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7190 (mpp80) REVERT: A 1154 ASP cc_start: 0.7879 (m-30) cc_final: 0.7446 (t0) REVERT: A 1168 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 1248 GLN cc_start: 0.8933 (tt0) cc_final: 0.8241 (tp40) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.2444 time to fit residues: 38.8240 Evaluate side-chains 110 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 104 optimal weight: 0.0270 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 3 optimal weight: 0.0000 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102596 restraints weight = 11886.249| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.90 r_work: 0.3082 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9500 Z= 0.102 Angle : 0.435 8.178 12857 Z= 0.223 Chirality : 0.037 0.132 1514 Planarity : 0.003 0.043 1608 Dihedral : 5.413 89.636 1391 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.48 % Allowed : 10.58 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1193 helix: 2.13 (0.19), residues: 782 sheet: -1.03 (0.72), residues: 58 loop : -0.12 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.011 0.001 PHE A 119 TYR 0.022 0.001 TYR A 248 ARG 0.005 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 617) hydrogen bonds : angle 3.86054 ( 1815) covalent geometry : bond 0.00209 ( 9500) covalent geometry : angle 0.43470 (12857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.958 Fit side-chains REVERT: A 165 ASP cc_start: 0.8524 (m-30) cc_final: 0.8164 (m-30) REVERT: A 604 ASN cc_start: 0.8628 (m-40) cc_final: 0.8409 (p0) REVERT: A 725 MET cc_start: 0.7128 (mmp) cc_final: 0.6726 (mtp) REVERT: A 756 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8660 (mp) REVERT: A 1046 ASP cc_start: 0.8058 (t70) cc_final: 0.7355 (t0) REVERT: A 1050 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6822 (mtp85) REVERT: A 1154 ASP cc_start: 0.7755 (m-30) cc_final: 0.7403 (t0) REVERT: A 1168 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7660 (mp) REVERT: A 1248 GLN cc_start: 0.8881 (tt0) cc_final: 0.8206 (tp40) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 0.2779 time to fit residues: 45.0765 Evaluate side-chains 113 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A1137 ASN A1242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095209 restraints weight = 11852.236| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.12 r_work: 0.2940 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9500 Z= 0.165 Angle : 0.496 9.762 12857 Z= 0.251 Chirality : 0.039 0.146 1514 Planarity : 0.003 0.041 1608 Dihedral : 5.421 84.263 1391 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.98 % Allowed : 11.77 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1193 helix: 1.90 (0.19), residues: 792 sheet: -1.21 (0.69), residues: 58 loop : -0.07 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.006 0.001 HIS A 103 PHE 0.018 0.001 PHE A 979 TYR 0.027 0.001 TYR A 248 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 617) hydrogen bonds : angle 3.97187 ( 1815) covalent geometry : bond 0.00389 ( 9500) covalent geometry : angle 0.49602 (12857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.996 Fit side-chains REVERT: A 40 GLU cc_start: 0.8070 (tp30) cc_final: 0.7664 (mt-10) REVERT: A 165 ASP cc_start: 0.8579 (m-30) cc_final: 0.8206 (m-30) REVERT: A 756 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 1046 ASP cc_start: 0.8057 (t70) cc_final: 0.7332 (t0) REVERT: A 1050 ARG cc_start: 0.7569 (mtp85) cc_final: 0.7064 (mtp85) REVERT: A 1154 ASP cc_start: 0.7808 (m-30) cc_final: 0.7444 (t0) REVERT: A 1168 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 1173 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5915 (pm20) REVERT: A 1248 GLN cc_start: 0.8877 (tt0) cc_final: 0.8131 (tp40) outliers start: 20 outliers final: 14 residues processed: 114 average time/residue: 0.2169 time to fit residues: 35.3194 Evaluate side-chains 111 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097623 restraints weight = 11796.902| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.01 r_work: 0.2966 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9500 Z= 0.123 Angle : 0.463 9.190 12857 Z= 0.233 Chirality : 0.037 0.128 1514 Planarity : 0.003 0.040 1608 Dihedral : 5.156 75.618 1391 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 12.86 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.25), residues: 1193 helix: 2.03 (0.19), residues: 790 sheet: -1.15 (0.69), residues: 58 loop : -0.08 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.005 0.001 HIS A 103 PHE 0.013 0.001 PHE A 979 TYR 0.023 0.001 TYR A 248 ARG 0.003 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 617) hydrogen bonds : angle 3.88054 ( 1815) covalent geometry : bond 0.00275 ( 9500) covalent geometry : angle 0.46271 (12857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.115 Fit side-chains REVERT: A 165 ASP cc_start: 0.8554 (m-30) cc_final: 0.8180 (m-30) REVERT: A 189 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: A 366 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 756 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 1046 ASP cc_start: 0.7996 (t70) cc_final: 0.7534 (t0) REVERT: A 1050 ARG cc_start: 0.7479 (mtp85) cc_final: 0.6969 (mtp85) REVERT: A 1154 ASP cc_start: 0.7751 (m-30) cc_final: 0.7385 (t0) REVERT: A 1168 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 1248 GLN cc_start: 0.8878 (tt0) cc_final: 0.8104 (tp40) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2376 time to fit residues: 38.2469 Evaluate side-chains 113 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097265 restraints weight = 11883.390| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.02 r_work: 0.2960 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9500 Z= 0.134 Angle : 0.472 9.366 12857 Z= 0.237 Chirality : 0.038 0.127 1514 Planarity : 0.003 0.039 1608 Dihedral : 4.654 53.884 1391 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.18 % Allowed : 12.86 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1193 helix: 2.03 (0.18), residues: 791 sheet: -1.12 (0.69), residues: 58 loop : -0.03 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.005 0.001 HIS A 103 PHE 0.015 0.001 PHE A 979 TYR 0.024 0.001 TYR A 248 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 617) hydrogen bonds : angle 3.86937 ( 1815) covalent geometry : bond 0.00306 ( 9500) covalent geometry : angle 0.47172 (12857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.000 Fit side-chains REVERT: A 40 GLU cc_start: 0.8074 (tp30) cc_final: 0.7585 (mt-10) REVERT: A 165 ASP cc_start: 0.8559 (m-30) cc_final: 0.8188 (m-30) REVERT: A 189 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 366 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 756 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 1046 ASP cc_start: 0.8023 (t70) cc_final: 0.7548 (t0) REVERT: A 1154 ASP cc_start: 0.7729 (m-30) cc_final: 0.7366 (t0) REVERT: A 1168 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 1173 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5889 (pm20) REVERT: A 1248 GLN cc_start: 0.8889 (tt0) cc_final: 0.8106 (tp40) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.2209 time to fit residues: 36.0226 Evaluate side-chains 114 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 chunk 50 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** 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 = 0.3620 r_free = 0.3620 target = 0.133618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098737 restraints weight = 11914.530| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.02 r_work: 0.3018 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9500 Z= 0.111 Angle : 0.451 8.811 12857 Z= 0.227 Chirality : 0.037 0.129 1514 Planarity : 0.003 0.039 1608 Dihedral : 3.999 45.966 1391 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 12.56 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1193 helix: 2.17 (0.19), residues: 786 sheet: -1.01 (0.70), residues: 58 loop : -0.06 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.012 0.001 PHE A 979 TYR 0.021 0.001 TYR A 248 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 617) hydrogen bonds : angle 3.79521 ( 1815) covalent geometry : bond 0.00240 ( 9500) covalent geometry : angle 0.45065 (12857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.055 Fit side-chains REVERT: A 40 GLU cc_start: 0.8065 (tp30) cc_final: 0.7621 (mt-10) REVERT: A 165 ASP cc_start: 0.8549 (m-30) cc_final: 0.8212 (m-30) REVERT: A 189 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 366 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 756 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 1046 ASP cc_start: 0.8039 (t70) cc_final: 0.7550 (t0) REVERT: A 1154 ASP cc_start: 0.7724 (m-30) cc_final: 0.7372 (t0) REVERT: A 1168 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 1173 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5870 (pm20) REVERT: A 1248 GLN cc_start: 0.8902 (tt0) cc_final: 0.8136 (tp40) outliers start: 27 outliers final: 19 residues processed: 119 average time/residue: 0.2164 time to fit residues: 36.5313 Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 114 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097389 restraints weight = 11760.200| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.10 r_work: 0.3007 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9500 Z= 0.111 Angle : 0.455 8.609 12857 Z= 0.229 Chirality : 0.037 0.128 1514 Planarity : 0.003 0.039 1608 Dihedral : 3.958 41.875 1391 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.57 % Allowed : 12.66 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.25), residues: 1193 helix: 2.23 (0.18), residues: 786 sheet: -0.93 (0.70), residues: 58 loop : -0.04 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.012 0.001 PHE A 979 TYR 0.022 0.001 TYR A 248 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 617) hydrogen bonds : angle 3.76553 ( 1815) covalent geometry : bond 0.00242 ( 9500) covalent geometry : angle 0.45524 (12857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.730 Fit side-chains REVERT: A 40 GLU cc_start: 0.8121 (tp30) cc_final: 0.7664 (mt-10) REVERT: A 165 ASP cc_start: 0.8581 (m-30) cc_final: 0.8237 (m-30) REVERT: A 189 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: A 366 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 621 SER cc_start: 0.7677 (m) cc_final: 0.7003 (p) REVERT: A 756 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8540 (mp) REVERT: A 1046 ASP cc_start: 0.8022 (t70) cc_final: 0.7547 (t0) REVERT: A 1154 ASP cc_start: 0.7715 (m-30) cc_final: 0.7343 (t0) REVERT: A 1168 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 1173 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: A 1248 GLN cc_start: 0.8919 (tt0) cc_final: 0.8160 (tp40) outliers start: 26 outliers final: 20 residues processed: 115 average time/residue: 0.2797 time to fit residues: 45.9450 Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1050 ARG Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 105 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100204 restraints weight = 11902.057| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.93 r_work: 0.3032 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9500 Z= 0.111 Angle : 0.458 8.523 12857 Z= 0.230 Chirality : 0.037 0.132 1514 Planarity : 0.003 0.039 1608 Dihedral : 3.923 37.203 1391 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.37 % Allowed : 12.76 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1193 helix: 2.26 (0.18), residues: 786 sheet: -0.88 (0.70), residues: 58 loop : -0.01 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.012 0.001 PHE A 979 TYR 0.022 0.001 TYR A 248 ARG 0.003 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 617) hydrogen bonds : angle 3.75976 ( 1815) covalent geometry : bond 0.00241 ( 9500) covalent geometry : angle 0.45774 (12857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.797 Fit side-chains REVERT: A 40 GLU cc_start: 0.8064 (tp30) cc_final: 0.7604 (mt-10) REVERT: A 165 ASP cc_start: 0.8538 (m-30) cc_final: 0.8200 (m-30) REVERT: A 189 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 366 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 604 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8360 (p0) REVERT: A 621 SER cc_start: 0.7587 (m) cc_final: 0.6863 (p) REVERT: A 756 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 1046 ASP cc_start: 0.7972 (t70) cc_final: 0.7663 (t0) REVERT: A 1154 ASP cc_start: 0.7670 (m-30) cc_final: 0.7297 (t0) REVERT: A 1168 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 1173 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5908 (pm20) REVERT: A 1248 GLN cc_start: 0.8894 (tt0) cc_final: 0.8135 (tp40) outliers start: 24 outliers final: 17 residues processed: 114 average time/residue: 0.2986 time to fit residues: 50.2862 Evaluate side-chains 116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096619 restraints weight = 11853.955| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.11 r_work: 0.2997 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9500 Z= 0.124 Angle : 0.464 8.813 12857 Z= 0.235 Chirality : 0.038 0.153 1514 Planarity : 0.003 0.036 1608 Dihedral : 3.954 35.496 1391 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 12.86 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1193 helix: 2.23 (0.18), residues: 788 sheet: -0.89 (0.70), residues: 58 loop : 0.01 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.005 0.001 HIS A 633 PHE 0.013 0.001 PHE A 979 TYR 0.023 0.001 TYR A 248 ARG 0.004 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 617) hydrogen bonds : angle 3.78222 ( 1815) covalent geometry : bond 0.00281 ( 9500) covalent geometry : angle 0.46449 (12857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.01 seconds wall clock time: 98 minutes 46.23 seconds (5926.23 seconds total)