Starting phenix.real_space_refine on Thu Jun 12 06:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0e_45081/06_2025/9c0e_45081_trim.cif" } resolution = 2.7 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= 0.001 sd= 0.025 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 P 12 5.49 5 Mg 2 5.21 5 S 77 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 8787 2.51 5 N 2290 2.21 5 O 2362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13538 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6716 Classifications: {'peptide': 909} Incomplete info: {'backbone_only': 26, 'truncation_to_alanine': 98} Link IDs: {'PTRANS': 31, 'TRANS': 877} Chain breaks: 2 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 7, 'TPO:plan-1': 3, 'ARG:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 24, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 243 Chain: "B" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6710 Classifications: {'peptide': 909} Incomplete info: {'backbone_only': 26, 'truncation_to_alanine': 100} Link IDs: {'PTRANS': 31, 'TRANS': 877} Chain breaks: 2 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 570 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 7, 'TPO:plan-1': 3, 'ARG:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 24, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 246 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' K': 1, ' CL': 1, ' MG': 1, ' NA': 1, 'ATP': 1, 'FUN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' K': 1, ' CL': 1, ' MG': 1, ' NA': 1, 'ATP': 1, 'FUN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 9.38, per 1000 atoms: 0.69 Number of scatterers: 13538 At special positions: 0 Unit cell: (114.758, 106.502, 146.131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 77 16.00 P 12 15.00 Mg 2 11.99 Na 2 11.00 O 2362 8.00 N 2290 7.00 C 8787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.7 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 2 sheets defined 64.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.582A pdb=" N LEU A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 305 " --> pdb=" O VAL A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 305' Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.505A pdb=" N LEU A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 397 removed outlier: 3.529A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.794A pdb=" N GLY A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.663A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 removed outlier: 3.583A pdb=" N THR A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 504 through 511 removed outlier: 4.917A pdb=" N GLY A 509 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 542 Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.737A pdb=" N THR A 555 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.825A pdb=" N LEU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.615A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.651A pdb=" N ASP A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 651 through 669 Processing helix chain 'A' and resid 673 through 699 removed outlier: 4.444A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 730 Processing helix chain 'A' and resid 731 through 753 Processing helix chain 'A' and resid 760 through 779 removed outlier: 3.588A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 801 through 811 removed outlier: 3.724A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 849 removed outlier: 3.972A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.511A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1015 removed outlier: 4.509A pdb=" N PHE A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1046 through 1050 Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1135 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1192 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.554A pdb=" N LEU B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 305 " --> pdb=" O VAL B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 305' Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 342 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 361 through 397 Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.858A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 removed outlier: 3.626A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 504 through 511 removed outlier: 5.127A pdb=" N GLY B 509 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 511 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 542 Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.520A pdb=" N LYS B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 599 through 632 Proline residue: B 623 - end of helix removed outlier: 3.668A pdb=" N ASP B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 4.864A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS B 643 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 Processing helix chain 'B' and resid 674 through 699 Processing helix chain 'B' and resid 712 through 730 Processing helix chain 'B' and resid 731 through 753 Processing helix chain 'B' and resid 760 through 778 removed outlier: 3.546A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.679A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 3.737A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 889 through 893 removed outlier: 4.654A pdb=" N LEU B 893 " --> pdb=" O LYS B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 913 Processing helix chain 'B' and resid 1003 through 1015 removed outlier: 4.589A pdb=" N PHE B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1046 through 1050 Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1121 through 1130 Processing helix chain 'B' and resid 1135 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing sheet with id=AA1, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.678A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A1054 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N MET A1087 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 854 through 859 removed outlier: 6.672A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY B 887 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B1197 " --> pdb=" O ARG B 921 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B1165 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B1024 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B1057 " --> pdb=" O ILE B1024 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B1026 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLY B1059 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B1054 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2442 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: 4.80 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4264 1.34 - 1.46: 3461 1.46 - 1.58: 5959 1.58 - 1.70: 34 1.70 - 1.82: 132 Bond restraints: 13850 Sorted by residual: bond pdb=" O1A ATP A1301 " pdb=" PA ATP A1301 " ideal model delta sigma weight residual 1.477 1.607 -0.130 1.10e-02 8.26e+03 1.40e+02 bond pdb=" O1A ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.477 1.607 -0.130 1.10e-02 8.26e+03 1.39e+02 bond pdb=" C6 ATP B1301 " pdb=" N6 ATP B1301 " ideal model delta sigma weight residual 1.337 1.442 -0.105 1.10e-02 8.26e+03 9.16e+01 bond pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 1.337 1.442 -0.105 1.10e-02 8.26e+03 9.12e+01 bond pdb=" O1B ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 1.477 1.605 -0.128 2.20e-02 2.07e+03 3.41e+01 ... (remaining 13845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 18799 3.88 - 7.77: 58 7.77 - 11.65: 13 11.65 - 15.54: 6 15.54 - 19.42: 3 Bond angle restraints: 18879 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 120.45 19.42 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 122.15 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 119.51 17.32 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 122.52 14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" N1 ATP B1301 " pdb=" C2 ATP B1301 " pdb=" N3 ATP B1301 " ideal model delta sigma weight residual 128.69 120.74 7.95 1.00e+00 1.00e+00 6.32e+01 ... (remaining 18874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6911 17.95 - 35.89: 814 35.89 - 53.84: 225 53.84 - 71.79: 35 71.79 - 89.73: 12 Dihedral angle restraints: 7997 sinusoidal: 2843 harmonic: 5154 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 32.73 60.27 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual 93.00 47.75 45.25 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 124.55 -31.55 1 1.00e+01 1.00e-02 1.42e+01 ... (remaining 7994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1414 0.029 - 0.058: 479 0.058 - 0.087: 187 0.087 - 0.116: 95 0.116 - 0.145: 7 Chirality restraints: 2182 Sorted by residual: chirality pdb=" C2' ATP B1301 " pdb=" C1' ATP B1301 " pdb=" C3' ATP B1301 " pdb=" O2' ATP B1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB TPO B 212 " pdb=" CA TPO B 212 " pdb=" OG1 TPO B 212 " pdb=" CG2 TPO B 212 " both_signs ideal model delta sigma weight residual False 2.48 2.62 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" C2' ATP A1301 " pdb=" C1' ATP A1301 " pdb=" C3' ATP A1301 " pdb=" O2' ATP A1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2179 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 513 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C ASP B 513 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP B 513 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO B 514 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 753 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO B 754 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 754 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 754 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 513 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 514 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.022 5.00e-02 4.00e+02 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.47: 71 2.47 - 3.14: 11173 3.14 - 3.81: 26634 3.81 - 4.47: 38681 4.47 - 5.14: 61188 Nonbonded interactions: 137747 Sorted by model distance: nonbonded pdb=" O2B ATP A1301 " pdb="MG MG A1306 " model vdw 1.803 2.170 nonbonded pdb=" O TRP A 300 " pdb="NA NA A1305 " model vdw 1.806 2.470 nonbonded pdb=" O GLY B 350 " pdb=" OG SER B 508 " model vdw 1.974 3.040 nonbonded pdb=" O GLY B 887 " pdb=" OH TYR B 903 " model vdw 1.985 3.040 nonbonded pdb=" O GLY A 887 " pdb=" OH TYR A 903 " model vdw 2.002 3.040 ... (remaining 137742 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 203 through 1125 or (resid 1126 through 1130 and (name N o \ r name CA or name C or name O or name CB )) or resid 1131 through 1212 or resid \ 1301 through 1306)) selection = chain 'B' } 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: 3.350 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.540 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 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 : 0.009 0.885 13855 Z= 0.823 Angle : 0.650 19.419 18887 Z= 0.407 Chirality : 0.038 0.145 2182 Planarity : 0.003 0.040 2347 Dihedral : 16.848 89.734 4705 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.51 % Allowed : 27.99 % Favored : 67.50 % 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: 2.11 (0.21), residues: 1788 helix: 2.88 (0.16), residues: 1018 sheet: 1.11 (0.50), residues: 120 loop : -1.10 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.002 0.001 HIS B 773 PHE 0.011 0.001 PHE A 811 TYR 0.010 0.001 TYR A 353 ARG 0.004 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.12654 ( 848) hydrogen bonds : angle 4.70046 ( 2442) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.38824 ( 8) covalent geometry : bond 0.00575 (13850) covalent geometry : angle 0.64994 (18879) Misc. bond : bond 0.88514 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 1.476 Fit side-chains REVERT: A 728 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7626 (t80) outliers start: 58 outliers final: 51 residues processed: 198 average time/residue: 0.8080 time to fit residues: 183.5612 Evaluate side-chains 193 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1135 THR Chi-restraints excluded: chain B residue 1193 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A1203 ASN B 229 HIS B1203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093791 restraints weight = 22309.049| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.82 r_work: 0.3076 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13855 Z= 0.134 Angle : 0.523 7.638 18887 Z= 0.277 Chirality : 0.041 0.174 2182 Planarity : 0.004 0.039 2347 Dihedral : 8.347 89.078 2082 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.75 % Allowed : 24.88 % Favored : 69.36 % 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: 1.82 (0.20), residues: 1788 helix: 2.46 (0.16), residues: 1038 sheet: 1.20 (0.50), residues: 116 loop : -0.99 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.014 0.001 PHE A 811 TYR 0.012 0.001 TYR B 353 ARG 0.006 0.001 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 848) hydrogen bonds : angle 4.11413 ( 2442) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.95538 ( 8) covalent geometry : bond 0.00288 (13850) covalent geometry : angle 0.52256 (18879) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 146 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8865 (mm) cc_final: 0.8631 (mm) REVERT: A 531 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8969 (mp) REVERT: A 728 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 785 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8311 (ptmm) REVERT: B 368 ILE cc_start: 0.8836 (mm) cc_final: 0.8626 (mm) REVERT: B 411 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9029 (mp) REVERT: B 531 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8980 (mp) REVERT: B 728 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 1151 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (tpt90) outliers start: 74 outliers final: 28 residues processed: 202 average time/residue: 0.8585 time to fit residues: 197.7730 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1151 ARG Chi-restraints excluded: chain B residue 1179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091489 restraints weight = 22734.713| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13855 Z= 0.180 Angle : 0.550 8.329 18887 Z= 0.291 Chirality : 0.042 0.155 2182 Planarity : 0.004 0.042 2347 Dihedral : 7.966 87.282 2041 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.75 % Allowed : 23.95 % Favored : 70.30 % 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: 1.56 (0.20), residues: 1788 helix: 2.23 (0.16), residues: 1040 sheet: 0.83 (0.48), residues: 116 loop : -1.02 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 733 HIS 0.002 0.001 HIS A 859 PHE 0.018 0.002 PHE B 811 TYR 0.013 0.001 TYR B 353 ARG 0.007 0.001 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 848) hydrogen bonds : angle 4.13220 ( 2442) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.97336 ( 8) covalent geometry : bond 0.00410 (13850) covalent geometry : angle 0.55007 (18879) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 139 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8948 (mm) cc_final: 0.8719 (mm) REVERT: A 531 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9021 (mp) REVERT: A 667 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8892 (mp) REVERT: A 728 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7698 (t80) REVERT: A 785 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8279 (ptmm) REVERT: A 1151 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8830 (tpt-90) REVERT: B 411 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9070 (mp) REVERT: B 531 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9016 (mp) REVERT: B 593 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: B 728 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 753 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8506 (ttmm) outliers start: 74 outliers final: 28 residues processed: 192 average time/residue: 0.8865 time to fit residues: 193.0145 Evaluate side-chains 175 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090334 restraints weight = 22593.316| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.82 r_work: 0.3007 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13855 Z= 0.213 Angle : 0.578 8.707 18887 Z= 0.306 Chirality : 0.043 0.147 2182 Planarity : 0.004 0.043 2347 Dihedral : 8.040 88.163 2038 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.75 % Allowed : 23.56 % Favored : 70.68 % 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: 1.39 (0.20), residues: 1788 helix: 2.10 (0.16), residues: 1038 sheet: 0.73 (0.47), residues: 116 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.003 0.001 HIS A1204 PHE 0.020 0.002 PHE B 811 TYR 0.013 0.002 TYR B 353 ARG 0.007 0.001 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 848) hydrogen bonds : angle 4.18682 ( 2442) SS BOND : bond 0.00104 ( 4) SS BOND : angle 1.27255 ( 8) covalent geometry : bond 0.00494 (13850) covalent geometry : angle 0.57724 (18879) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 139 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8973 (mm) cc_final: 0.8749 (mm) REVERT: A 531 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9011 (mp) REVERT: A 667 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 728 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7664 (t80) REVERT: A 785 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8318 (ptmm) REVERT: A 850 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8829 (mmtm) REVERT: A 865 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 898 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7985 (mtp85) REVERT: A 1151 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8861 (tpt-90) REVERT: B 368 ILE cc_start: 0.8939 (mm) cc_final: 0.8738 (mm) REVERT: B 411 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 531 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9011 (mp) REVERT: B 728 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 753 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8554 (ttmm) outliers start: 74 outliers final: 38 residues processed: 194 average time/residue: 0.8838 time to fit residues: 194.4700 Evaluate side-chains 178 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1180 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain B residue 1191 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092231 restraints weight = 22710.870| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.83 r_work: 0.3050 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13855 Z= 0.149 Angle : 0.538 8.444 18887 Z= 0.282 Chirality : 0.041 0.146 2182 Planarity : 0.004 0.042 2347 Dihedral : 7.772 89.008 2038 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.90 % Allowed : 24.26 % Favored : 70.84 % 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: 1.48 (0.20), residues: 1788 helix: 2.19 (0.16), residues: 1038 sheet: 0.78 (0.48), residues: 116 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 733 HIS 0.002 0.001 HIS B 695 PHE 0.015 0.001 PHE A 811 TYR 0.014 0.001 TYR B 353 ARG 0.006 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 848) hydrogen bonds : angle 4.08773 ( 2442) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.39630 ( 8) covalent geometry : bond 0.00332 (13850) covalent geometry : angle 0.53745 (18879) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 137 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 531 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9017 (mp) REVERT: A 728 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 785 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8293 (ptmm) REVERT: A 850 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8785 (mmtm) REVERT: A 865 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: A 1151 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8861 (tpt-90) REVERT: B 368 ILE cc_start: 0.8888 (mm) cc_final: 0.8666 (mm) REVERT: B 411 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9009 (mp) REVERT: B 728 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 753 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8543 (ttmm) outliers start: 63 outliers final: 32 residues processed: 181 average time/residue: 0.9225 time to fit residues: 189.2177 Evaluate side-chains 169 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain B residue 1191 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089211 restraints weight = 22846.878| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13855 Z= 0.262 Angle : 0.616 9.211 18887 Z= 0.325 Chirality : 0.044 0.157 2182 Planarity : 0.004 0.044 2347 Dihedral : 8.124 88.897 2037 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.83 % Allowed : 23.33 % Favored : 70.84 % 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: 1.14 (0.20), residues: 1788 helix: 1.92 (0.16), residues: 1052 sheet: 0.17 (0.45), residues: 128 loop : -1.25 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 733 HIS 0.003 0.001 HIS A 806 PHE 0.021 0.002 PHE B 811 TYR 0.015 0.002 TYR B1041 ARG 0.006 0.001 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.06005 ( 848) hydrogen bonds : angle 4.24824 ( 2442) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.22234 ( 8) covalent geometry : bond 0.00610 (13850) covalent geometry : angle 0.61584 (18879) Misc. bond : bond 0.00130 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7764 (tpp80) REVERT: A 531 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8994 (mp) REVERT: A 728 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7658 (t80) REVERT: A 785 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8283 (ptmm) REVERT: A 850 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8819 (mmtm) REVERT: A 865 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: A 905 ASN cc_start: 0.9165 (m110) cc_final: 0.8940 (m-40) REVERT: A 1151 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8853 (tpt-90) REVERT: B 368 ILE cc_start: 0.8968 (mm) cc_final: 0.8746 (mm) REVERT: B 411 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9102 (mp) REVERT: B 728 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7834 (t80) outliers start: 75 outliers final: 39 residues processed: 192 average time/residue: 0.8946 time to fit residues: 194.8016 Evaluate side-chains 180 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1180 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain B residue 1191 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 174 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093384 restraints weight = 22561.111| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.84 r_work: 0.3066 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13855 Z= 0.126 Angle : 0.531 9.435 18887 Z= 0.276 Chirality : 0.040 0.144 2182 Planarity : 0.004 0.042 2347 Dihedral : 7.598 89.899 2037 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.89 % Allowed : 25.66 % Favored : 70.45 % 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: 1.45 (0.20), residues: 1788 helix: 2.19 (0.16), residues: 1046 sheet: 0.90 (0.48), residues: 116 loop : -1.22 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.012 0.001 PHE A 811 TYR 0.014 0.001 TYR B 353 ARG 0.007 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 848) hydrogen bonds : angle 4.06838 ( 2442) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.93212 ( 8) covalent geometry : bond 0.00269 (13850) covalent geometry : angle 0.53118 (18879) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 728 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7694 (t80) REVERT: A 785 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8250 (ptmm) REVERT: A 850 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8811 (mmtm) REVERT: A 865 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: B 411 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8988 (mp) REVERT: B 728 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7870 (t80) outliers start: 50 outliers final: 25 residues processed: 176 average time/residue: 0.9157 time to fit residues: 182.4428 Evaluate side-chains 159 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1129 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089887 restraints weight = 22707.605| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.83 r_work: 0.3001 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13855 Z= 0.236 Angle : 0.609 9.788 18887 Z= 0.320 Chirality : 0.044 0.200 2182 Planarity : 0.004 0.043 2347 Dihedral : 7.927 89.453 2035 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.28 % Allowed : 25.51 % Favored : 70.22 % 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: 1.22 (0.20), residues: 1788 helix: 2.01 (0.16), residues: 1048 sheet: 0.28 (0.46), residues: 128 loop : -1.25 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 733 HIS 0.003 0.001 HIS A1204 PHE 0.020 0.002 PHE B 811 TYR 0.015 0.002 TYR B 353 ARG 0.007 0.001 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 848) hydrogen bonds : angle 4.20555 ( 2442) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.04540 ( 8) covalent geometry : bond 0.00548 (13850) covalent geometry : angle 0.60836 (18879) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7732 (tpp80) REVERT: A 667 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8889 (mp) REVERT: A 728 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 785 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: A 850 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8803 (mmtm) REVERT: A 865 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: B 411 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 531 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8988 (mp) REVERT: B 728 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7863 (t80) REVERT: B 753 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8461 (ttmm) outliers start: 55 outliers final: 29 residues processed: 172 average time/residue: 1.0299 time to fit residues: 198.6077 Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain B residue 1191 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092808 restraints weight = 22518.081| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.83 r_work: 0.3061 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13855 Z= 0.139 Angle : 0.551 9.832 18887 Z= 0.286 Chirality : 0.040 0.151 2182 Planarity : 0.004 0.051 2347 Dihedral : 7.602 89.939 2035 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.88 % Allowed : 27.06 % Favored : 70.06 % 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: 1.39 (0.20), residues: 1788 helix: 2.17 (0.16), residues: 1046 sheet: 0.43 (0.47), residues: 128 loop : -1.23 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.014 0.001 PHE A 811 TYR 0.014 0.001 TYR B 353 ARG 0.010 0.001 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 848) hydrogen bonds : angle 4.08330 ( 2442) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.90414 ( 8) covalent geometry : bond 0.00305 (13850) covalent geometry : angle 0.55089 (18879) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7684 (tpp80) REVERT: A 728 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 785 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8282 (ptmm) REVERT: A 865 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: B 411 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8999 (mp) REVERT: B 728 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 753 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8431 (ttmm) outliers start: 37 outliers final: 20 residues processed: 158 average time/residue: 1.0449 time to fit residues: 187.6431 Evaluate side-chains 155 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS B 814 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093283 restraints weight = 22522.796| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.83 r_work: 0.3069 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13855 Z= 0.137 Angle : 0.549 10.573 18887 Z= 0.283 Chirality : 0.040 0.137 2182 Planarity : 0.004 0.054 2347 Dihedral : 7.480 89.396 2033 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.64 % Allowed : 27.37 % Favored : 69.98 % 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: 1.46 (0.20), residues: 1788 helix: 2.16 (0.16), residues: 1058 sheet: 0.97 (0.49), residues: 116 loop : -1.24 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.014 0.001 PHE A 811 TYR 0.014 0.001 TYR B 353 ARG 0.012 0.001 ARG A 828 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 848) hydrogen bonds : angle 4.01822 ( 2442) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.86095 ( 8) covalent geometry : bond 0.00302 (13850) covalent geometry : angle 0.54858 (18879) Misc. bond : bond 0.00044 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7665 (tpp80) REVERT: A 728 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7635 (t80) REVERT: A 785 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8254 (ptmm) REVERT: A 865 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: B 411 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8980 (mp) REVERT: B 728 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7934 (t80) REVERT: B 753 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8422 (ttmm) outliers start: 34 outliers final: 20 residues processed: 168 average time/residue: 0.9543 time to fit residues: 180.8876 Evaluate side-chains 154 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092855 restraints weight = 22769.253| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.84 r_work: 0.3053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 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 : 0.003 0.046 13855 Z= 0.150 Angle : 0.560 10.843 18887 Z= 0.289 Chirality : 0.041 0.138 2182 Planarity : 0.004 0.060 2347 Dihedral : 7.536 89.155 2033 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.72 % Allowed : 27.68 % Favored : 69.60 % 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: 1.53 (0.20), residues: 1788 helix: 2.22 (0.16), residues: 1048 sheet: 0.99 (0.49), residues: 116 loop : -1.17 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.015 0.001 PHE A 811 TYR 0.014 0.001 TYR B 353 ARG 0.012 0.001 ARG A 828 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 848) hydrogen bonds : angle 4.03850 ( 2442) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.90631 ( 8) covalent geometry : bond 0.00337 (13850) covalent geometry : angle 0.55988 (18879) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9219.67 seconds wall clock time: 157 minutes 40.29 seconds (9460.29 seconds total)