Starting phenix.real_space_refine on Fri Jul 25 09:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.map" model { file = "/net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c08_45076/07_2025/9c08_45076.cif" } resolution = 2.96 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4892 2.51 5 N 1172 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7420 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1855 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 2 Restraints were copied for chains: C, B, D Time building chain proxies: 3.81, per 1000 atoms: 0.51 Number of scatterers: 7420 At special positions: 0 Unit cell: (111.1, 111.1, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1336 8.00 N 1172 7.00 C 4892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 47.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.520A pdb=" N LEU A 22 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.517A pdb=" N PHE A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.677A pdb=" N THR A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 removed outlier: 3.532A pdb=" N GLN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.584A pdb=" N ASN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.831A pdb=" N ASP A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 260 through 267 removed outlier: 4.267A pdb=" N TYR A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 265 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.520A pdb=" N LEU B 22 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.517A pdb=" N PHE B 44 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 45' Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.677A pdb=" N THR B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 removed outlier: 3.532A pdb=" N GLN B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.584A pdb=" N ASN B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 199 through 215 removed outlier: 3.831A pdb=" N ASP B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 260 through 267 removed outlier: 4.267A pdb=" N TYR B 264 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 265 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.520A pdb=" N LEU C 22 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER C 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.517A pdb=" N PHE C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.677A pdb=" N THR C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.532A pdb=" N GLN C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 121 through 136 removed outlier: 3.584A pdb=" N ASN C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 199 through 215 removed outlier: 3.831A pdb=" N ASP C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 260 through 267 removed outlier: 4.267A pdb=" N TYR C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 265 " --> pdb=" O HIS C 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.520A pdb=" N LEU D 22 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.517A pdb=" N PHE D 44 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 45' Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.677A pdb=" N THR D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 removed outlier: 3.532A pdb=" N GLN D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 121 through 136 removed outlier: 3.584A pdb=" N ASN D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 199 through 215 removed outlier: 3.831A pdb=" N ASP D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 260 through 267 removed outlier: 4.267A pdb=" N TYR D 264 " --> pdb=" O PRO D 260 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 265 " --> pdb=" O HIS D 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 112 removed outlier: 9.018A pdb=" N LYS A 53 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ASN A 84 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 55 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 86 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 57 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 36 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 57 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 38 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 59 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 35 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS A 39 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 13 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR A 160 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 15 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 111 through 112 removed outlier: 9.018A pdb=" N LYS B 53 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ASN B 84 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS B 55 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 86 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 57 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 36 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 57 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG B 38 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE B 59 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 35 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS B 39 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 13 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR B 160 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL B 15 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 111 through 112 removed outlier: 9.018A pdb=" N LYS C 53 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ASN C 84 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS C 55 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 86 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 57 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 36 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 57 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 38 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE C 59 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 35 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS C 39 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 13 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR C 160 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 15 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 111 through 112 removed outlier: 9.018A pdb=" N LYS D 53 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ASN D 84 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS D 55 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE D 86 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 57 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL D 36 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 57 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG D 38 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE D 59 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 35 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS D 39 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 13 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 160 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL D 15 " --> pdb=" O THR D 160 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 636 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: 2.22 Time building geometry restraints manager: 2.15 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: 2268 1.34 - 1.46: 1952 1.46 - 1.58: 3384 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 7636 Sorted by residual: bond pdb=" N ASN B 251 " pdb=" CA ASN B 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N ASN A 251 " pdb=" CA ASN A 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N ASN C 251 " pdb=" CA ASN C 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N ASN D 251 " pdb=" CA ASN D 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N GLY A 17 " pdb=" CA GLY A 17 " ideal model delta sigma weight residual 1.438 1.448 -0.010 1.41e-02 5.03e+03 5.07e-01 ... (remaining 7631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.59: 9076 0.59 - 1.18: 1024 1.18 - 1.77: 156 1.77 - 2.36: 40 2.36 - 2.95: 56 Bond angle restraints: 10352 Sorted by residual: angle pdb=" N ILE B 202 " pdb=" CA ILE B 202 " pdb=" C ILE B 202 " ideal model delta sigma weight residual 111.90 109.01 2.89 8.10e-01 1.52e+00 1.28e+01 angle pdb=" N ILE C 202 " pdb=" CA ILE C 202 " pdb=" C ILE C 202 " ideal model delta sigma weight residual 111.90 109.01 2.89 8.10e-01 1.52e+00 1.28e+01 angle pdb=" N ILE D 202 " pdb=" CA ILE D 202 " pdb=" C ILE D 202 " ideal model delta sigma weight residual 111.90 109.01 2.89 8.10e-01 1.52e+00 1.28e+01 angle pdb=" N ILE A 202 " pdb=" CA ILE A 202 " pdb=" C ILE A 202 " ideal model delta sigma weight residual 111.90 109.01 2.89 8.10e-01 1.52e+00 1.28e+01 angle pdb=" CA GLY C 17 " pdb=" C GLY C 17 " pdb=" N ASN C 18 " ideal model delta sigma weight residual 115.27 116.98 -1.71 7.60e-01 1.73e+00 5.07e+00 ... (remaining 10347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.33: 4156 11.33 - 22.66: 216 22.66 - 33.99: 88 33.99 - 45.32: 8 45.32 - 56.66: 4 Dihedral angle restraints: 4472 sinusoidal: 1796 harmonic: 2676 Sorted by residual: dihedral pdb=" CB LYS B 200 " pdb=" CG LYS B 200 " pdb=" CD LYS B 200 " pdb=" CE LYS B 200 " ideal model delta sinusoidal sigma weight residual 60.00 116.66 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS A 200 " pdb=" CG LYS A 200 " pdb=" CD LYS A 200 " pdb=" CE LYS A 200 " ideal model delta sinusoidal sigma weight residual 60.00 116.66 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS C 200 " pdb=" CG LYS C 200 " pdb=" CD LYS C 200 " pdb=" CE LYS C 200 " ideal model delta sinusoidal sigma weight residual 60.00 116.66 -56.66 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 4469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 568 0.028 - 0.056: 352 0.056 - 0.084: 100 0.084 - 0.112: 72 0.112 - 0.140: 16 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 233 " pdb=" N ILE A 233 " pdb=" C ILE A 233 " pdb=" CB ILE A 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 233 " pdb=" N ILE B 233 " pdb=" C ILE B 233 " pdb=" CB ILE B 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1105 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 259 " -0.015 5.00e-02 4.00e+02 2.34e-02 8.75e-01 pdb=" N PRO B 260 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 260 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 260 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 259 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.75e-01 pdb=" N PRO A 260 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 259 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.75e-01 pdb=" N PRO D 260 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO D 260 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 260 " 0.013 5.00e-02 4.00e+02 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2032 2.81 - 3.33: 6180 3.33 - 3.85: 11128 3.85 - 4.38: 13287 4.38 - 4.90: 23917 Nonbonded interactions: 56544 Sorted by model distance: nonbonded pdb=" OD1 ASN A 136 " pdb=" NZ LYS B 266 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASN B 136 " pdb=" NZ LYS C 266 " model vdw 2.284 3.120 nonbonded pdb=" NZ LYS A 266 " pdb=" OD1 ASN D 136 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASN C 136 " pdb=" NZ LYS D 266 " model vdw 2.285 3.120 nonbonded pdb=" OG SER C 21 " pdb=" OD1 ASP C 163 " model vdw 2.364 3.040 ... (remaining 56539 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 36.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:52.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.002 0.034 7636 Z= 0.093 Angle : 0.442 2.950 10352 Z= 0.276 Chirality : 0.044 0.140 1108 Planarity : 0.003 0.023 1308 Dihedral : 8.367 56.655 2760 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.47 % Allowed : 3.43 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 868 helix: 1.05 (0.35), residues: 264 sheet: 1.25 (0.50), residues: 108 loop : 0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 117 PHE 0.007 0.001 PHE A 262 TYR 0.011 0.001 TYR B 127 ARG 0.001 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.21687 ( 232) hydrogen bonds : angle 6.40590 ( 636) covalent geometry : bond 0.00185 ( 7636) covalent geometry : angle 0.44211 (10352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.787 Fit side-chains REVERT: A 266 LYS cc_start: 0.7975 (ptpt) cc_final: 0.7765 (ptpt) outliers start: 12 outliers final: 4 residues processed: 147 average time/residue: 1.5963 time to fit residues: 246.7232 Evaluate side-chains 88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 104 GLN A 112 ASN A 212 GLN B 104 GLN B 112 ASN B 212 GLN C 104 GLN C 112 ASN C 212 GLN D 104 GLN D 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138052 restraints weight = 7458.798| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.17 r_work: 0.3426 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7636 Z= 0.126 Angle : 0.504 4.083 10352 Z= 0.277 Chirality : 0.047 0.154 1108 Planarity : 0.004 0.023 1308 Dihedral : 4.011 19.714 992 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.96 % Allowed : 8.70 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 868 helix: 1.08 (0.32), residues: 300 sheet: 1.02 (0.48), residues: 108 loop : 0.00 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE D 218 TYR 0.015 0.001 TYR D 127 ARG 0.005 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 232) hydrogen bonds : angle 3.92250 ( 636) covalent geometry : bond 0.00297 ( 7636) covalent geometry : angle 0.50426 (10352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.868 Fit side-chains REVERT: A 24 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: B 24 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: C 24 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7563 (mt0) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 1.4253 time to fit residues: 158.4967 Evaluate side-chains 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 102 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 83 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 212 GLN C 212 GLN D 211 GLN D 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139261 restraints weight = 7617.725| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.31 r_work: 0.3421 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7636 Z= 0.101 Angle : 0.461 3.561 10352 Z= 0.253 Chirality : 0.046 0.144 1108 Planarity : 0.003 0.024 1308 Dihedral : 4.004 20.112 992 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.94 % Allowed : 9.68 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 868 helix: 1.22 (0.32), residues: 300 sheet: 0.96 (0.47), residues: 108 loop : -0.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 213 PHE 0.009 0.001 PHE B 218 TYR 0.013 0.001 TYR D 127 ARG 0.005 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 232) hydrogen bonds : angle 3.68794 ( 636) covalent geometry : bond 0.00236 ( 7636) covalent geometry : angle 0.46122 (10352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.768 Fit side-chains REVERT: A 24 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7563 (mt0) REVERT: A 66 GLU cc_start: 0.8396 (mp0) cc_final: 0.8159 (mp0) REVERT: B 24 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 66 GLU cc_start: 0.8401 (mp0) cc_final: 0.8163 (mp0) REVERT: C 24 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: C 66 GLU cc_start: 0.8402 (mp0) cc_final: 0.8163 (mp0) REVERT: D 24 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7075 (mt0) outliers start: 24 outliers final: 5 residues processed: 98 average time/residue: 1.6119 time to fit residues: 165.2378 Evaluate side-chains 99 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 102 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 73 HIS B 212 GLN C 73 HIS C 212 GLN D 73 HIS D 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.172263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135756 restraints weight = 7478.716| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.32 r_work: 0.3402 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7636 Z= 0.114 Angle : 0.482 4.216 10352 Z= 0.264 Chirality : 0.046 0.148 1108 Planarity : 0.003 0.025 1308 Dihedral : 4.023 19.735 989 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.96 % Allowed : 10.42 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 868 helix: 1.13 (0.31), residues: 300 sheet: 0.93 (0.49), residues: 108 loop : -0.31 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 213 PHE 0.011 0.001 PHE D 218 TYR 0.014 0.001 TYR D 127 ARG 0.006 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 232) hydrogen bonds : angle 3.72604 ( 636) covalent geometry : bond 0.00272 ( 7636) covalent geometry : angle 0.48153 (10352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.791 Fit side-chains REVERT: A 24 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: B 24 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: C 24 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: D 24 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7001 (mt0) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 1.6042 time to fit residues: 160.7606 Evaluate side-chains 104 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 227 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 59 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137241 restraints weight = 7554.359| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.09 r_work: 0.3426 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7636 Z= 0.089 Angle : 0.442 3.937 10352 Z= 0.243 Chirality : 0.045 0.142 1108 Planarity : 0.003 0.026 1308 Dihedral : 3.892 19.630 989 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.96 % Allowed : 10.91 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 868 helix: 1.26 (0.31), residues: 300 sheet: 0.94 (0.48), residues: 108 loop : -0.28 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 213 PHE 0.007 0.001 PHE B 218 TYR 0.012 0.001 TYR D 127 ARG 0.006 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 232) hydrogen bonds : angle 3.64086 ( 636) covalent geometry : bond 0.00206 ( 7636) covalent geometry : angle 0.44200 (10352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.817 Fit side-chains REVERT: A 24 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: B 24 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: C 24 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: D 24 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6978 (mt0) outliers start: 16 outliers final: 8 residues processed: 100 average time/residue: 1.4629 time to fit residues: 153.4284 Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 102 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 212 GLN C 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134626 restraints weight = 7548.894| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.08 r_work: 0.3417 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7636 Z= 0.102 Angle : 0.462 3.716 10352 Z= 0.254 Chirality : 0.045 0.146 1108 Planarity : 0.003 0.027 1308 Dihedral : 3.946 19.742 989 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.45 % Allowed : 11.76 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 868 helix: 1.19 (0.31), residues: 300 sheet: 0.87 (0.49), residues: 108 loop : -0.31 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 213 PHE 0.009 0.001 PHE C 218 TYR 0.013 0.001 TYR D 127 ARG 0.006 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 232) hydrogen bonds : angle 3.71488 ( 636) covalent geometry : bond 0.00243 ( 7636) covalent geometry : angle 0.46219 (10352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.820 Fit side-chains REVERT: A 24 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: B 24 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: C 24 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: D 24 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7051 (mt0) outliers start: 20 outliers final: 11 residues processed: 103 average time/residue: 1.4015 time to fit residues: 151.5123 Evaluate side-chains 108 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 227 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131600 restraints weight = 7521.123| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.20 r_work: 0.3373 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7636 Z= 0.126 Angle : 0.492 3.763 10352 Z= 0.270 Chirality : 0.046 0.146 1108 Planarity : 0.003 0.027 1308 Dihedral : 4.114 19.855 989 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.96 % Allowed : 12.38 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 868 helix: 1.24 (0.30), residues: 292 sheet: 0.76 (0.49), residues: 108 loop : -0.33 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 213 PHE 0.009 0.001 PHE C 218 TYR 0.014 0.001 TYR D 127 ARG 0.006 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 232) hydrogen bonds : angle 3.87896 ( 636) covalent geometry : bond 0.00305 ( 7636) covalent geometry : angle 0.49157 (10352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.790 Fit side-chains REVERT: A 24 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: B 24 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: C 24 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: D 24 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7027 (mt0) outliers start: 16 outliers final: 4 residues processed: 100 average time/residue: 1.3537 time to fit residues: 142.4900 Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.0670 chunk 87 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134775 restraints weight = 7684.059| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.19 r_work: 0.3412 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7636 Z= 0.098 Angle : 0.450 3.635 10352 Z= 0.249 Chirality : 0.045 0.136 1108 Planarity : 0.003 0.027 1308 Dihedral : 3.971 19.588 989 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.47 % Allowed : 14.22 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 868 helix: 1.40 (0.31), residues: 292 sheet: 0.76 (0.49), residues: 108 loop : -0.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 213 PHE 0.008 0.001 PHE A 218 TYR 0.012 0.001 TYR D 127 ARG 0.007 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 232) hydrogen bonds : angle 3.80131 ( 636) covalent geometry : bond 0.00230 ( 7636) covalent geometry : angle 0.45050 (10352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.806 Fit side-chains REVERT: A 24 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: A 66 GLU cc_start: 0.8358 (mp0) cc_final: 0.8117 (mp0) REVERT: B 24 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: B 66 GLU cc_start: 0.8357 (mp0) cc_final: 0.8118 (mp0) REVERT: C 24 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 66 GLU cc_start: 0.8363 (mp0) cc_final: 0.8097 (mp0) REVERT: D 24 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7008 (mt0) outliers start: 12 outliers final: 4 residues processed: 98 average time/residue: 1.2250 time to fit residues: 126.8793 Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131812 restraints weight = 7629.622| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.21 r_work: 0.3392 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7636 Z= 0.115 Angle : 0.476 3.867 10352 Z= 0.262 Chirality : 0.046 0.135 1108 Planarity : 0.003 0.027 1308 Dihedral : 4.081 19.792 989 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.47 % Allowed : 14.22 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 868 helix: 1.38 (0.30), residues: 292 sheet: 0.68 (0.48), residues: 108 loop : -0.36 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 213 PHE 0.009 0.001 PHE C 218 TYR 0.014 0.001 TYR D 127 ARG 0.007 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 232) hydrogen bonds : angle 3.91369 ( 636) covalent geometry : bond 0.00276 ( 7636) covalent geometry : angle 0.47559 (10352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.831 Fit side-chains REVERT: A 24 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: B 24 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: C 24 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: D 24 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7035 (mt0) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 1.3423 time to fit residues: 126.4355 Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138053 restraints weight = 7755.109| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.07 r_work: 0.3440 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7636 Z= 0.093 Angle : 0.448 4.010 10352 Z= 0.248 Chirality : 0.045 0.134 1108 Planarity : 0.003 0.028 1308 Dihedral : 3.963 19.582 989 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.10 % Allowed : 14.58 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 868 helix: 1.48 (0.31), residues: 292 sheet: 0.73 (0.49), residues: 108 loop : -0.29 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 213 PHE 0.008 0.001 PHE B 218 TYR 0.012 0.001 TYR D 127 ARG 0.007 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 232) hydrogen bonds : angle 3.83775 ( 636) covalent geometry : bond 0.00218 ( 7636) covalent geometry : angle 0.44781 (10352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.838 Fit side-chains REVERT: A 24 GLN cc_start: 0.7768 (mt0) cc_final: 0.7552 (mt0) REVERT: A 76 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7132 (ttm-80) REVERT: B 24 GLN cc_start: 0.7762 (mt0) cc_final: 0.7547 (mt0) REVERT: B 76 ARG cc_start: 0.7498 (ttt90) cc_final: 0.7151 (ttm-80) REVERT: C 24 GLN cc_start: 0.7742 (mt0) cc_final: 0.7531 (mt0) REVERT: C 76 ARG cc_start: 0.7490 (ttt90) cc_final: 0.7137 (ttm-80) REVERT: D 24 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6945 (mt0) REVERT: D 76 ARG cc_start: 0.7481 (ttt90) cc_final: 0.7139 (ttm-80) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 1.1672 time to fit residues: 123.6998 Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.169179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133456 restraints weight = 7555.549| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.19 r_work: 0.3410 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7636 Z= 0.099 Angle : 0.454 3.871 10352 Z= 0.251 Chirality : 0.045 0.135 1108 Planarity : 0.003 0.027 1308 Dihedral : 3.974 19.637 989 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.98 % Allowed : 14.71 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 868 helix: 1.52 (0.31), residues: 292 sheet: 0.73 (0.49), residues: 108 loop : -0.33 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 213 PHE 0.008 0.001 PHE C 218 TYR 0.013 0.001 TYR D 127 ARG 0.007 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 232) hydrogen bonds : angle 3.85453 ( 636) covalent geometry : bond 0.00234 ( 7636) covalent geometry : angle 0.45370 (10352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5197.70 seconds wall clock time: 90 minutes 24.77 seconds (5424.77 seconds total)