Starting phenix.real_space_refine on Wed Sep 17 11:43:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jjn_61533/09_2025/9jjn_61533.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 5382 2.51 5 N 1421 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8358 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8250 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.23 Number of scatterers: 8358 At special positions: 0 Unit cell: (73.87, 90.47, 166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1491 8.00 N 1421 7.00 C 5382 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A1202 " " NAG C 1 " - " ASN A1205 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 301.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 58.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 44 removed outlier: 3.624A pdb=" N CYS A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.546A pdb=" N ALA A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 122 removed outlier: 3.583A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.605A pdb=" N ARG A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.533A pdb=" N ASN A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.620A pdb=" N VAL A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 323 removed outlier: 5.281A pdb=" N GLN A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.810A pdb=" N SER A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 578 through 594 removed outlier: 3.779A pdb=" N LEU A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 595 through 616 removed outlier: 3.538A pdb=" N ARG A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.624A pdb=" N ALA A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.503A pdb=" N LYS A 644 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 removed outlier: 4.101A pdb=" N GLU A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 744 removed outlier: 3.979A pdb=" N SER A 743 " --> pdb=" O ARG A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.622A pdb=" N LEU A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 858 through 869 removed outlier: 3.669A pdb=" N LYS A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 979 through 993 Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 3.519A pdb=" N SER A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1071 through 1073 No H-bonds generated for 'chain 'A' and resid 1071 through 1073' Processing helix chain 'A' and resid 1074 through 1113 Processing helix chain 'A' and resid 1120 through 1138 Proline residue: A1133 - end of helix removed outlier: 3.581A pdb=" N SER A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1147 through 1151 removed outlier: 3.887A pdb=" N MET A1151 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1201 removed outlier: 3.585A pdb=" N GLN A1165 " --> pdb=" O PRO A1161 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU A1178 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A1199 " --> pdb=" O CYS A1195 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A1200 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1251 removed outlier: 3.793A pdb=" N THR A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 removed outlier: 3.686A pdb=" N THR A1265 " --> pdb=" O SER A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1265' Processing helix chain 'A' and resid 1266 through 1291 Proline residue: A1274 - end of helix Processing helix chain 'A' and resid 1301 through 1305 removed outlier: 3.763A pdb=" N VAL A1305 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1348 removed outlier: 3.755A pdb=" N TRP A1310 " --> pdb=" O PRO A1306 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A1321 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A1323 " --> pdb=" O LEU A1319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A1337 " --> pdb=" O ARG A1333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178 removed outlier: 4.232A pdb=" N TRP A 167 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 187 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 241 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'A' and resid 878 through 880 removed outlier: 6.618A pdb=" N ILE A 879 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N PHE A 975 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A 853 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 997 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE A1019 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS A 999 " --> pdb=" O ILE A1019 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A1021 " --> pdb=" O CYS A 999 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A1001 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER A1018 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE A1067 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA A1020 " --> pdb=" O PHE A1067 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 557 removed outlier: 6.241A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 435 " --> pdb=" O MET A 824 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N MET A 824 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN A 821 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY A 825 " --> pdb=" O TRP A 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 552 through 557 removed outlier: 6.241A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 435 " --> pdb=" O MET A 824 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N MET A 824 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET A 824 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE A 749 " --> pdb=" O MET A 824 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET A 826 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 747 " --> pdb=" O MET A 826 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER A 828 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR A 745 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 752 " --> pdb=" O MET A 700 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 683 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 691 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN A 649 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ILE A 767 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 654 " --> pdb=" O ILE A 767 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 769 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A 656 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757 476 hydrogen bonds defined for protein. 1380 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: 1.50 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1496 1.33 - 1.45: 2091 1.45 - 1.57: 4869 1.57 - 1.69: 3 1.69 - 1.82: 85 Bond restraints: 8544 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CG PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 1.503 1.365 0.138 3.40e-02 8.65e+02 1.64e+01 bond pdb=" CB PRO A 427 " pdb=" CG PRO A 427 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" N PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 1.473 1.499 -0.026 1.40e-02 5.10e+03 3.37e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.82e+00 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11559 3.08 - 6.16: 36 6.16 - 9.24: 3 9.24 - 12.32: 2 12.32 - 15.40: 1 Bond angle restraints: 11601 Sorted by residual: angle pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 112.00 96.60 15.40 1.40e+00 5.10e-01 1.21e+02 angle pdb=" N PRO A 427 " pdb=" CD PRO A 427 " pdb=" CG PRO A 427 " ideal model delta sigma weight residual 103.20 91.78 11.42 1.50e+00 4.44e-01 5.80e+01 angle pdb=" CA PRO A 427 " pdb=" CB PRO A 427 " pdb=" CG PRO A 427 " ideal model delta sigma weight residual 104.50 96.72 7.78 1.90e+00 2.77e-01 1.68e+01 angle pdb=" CB MET A 754 " pdb=" CG MET A 754 " pdb=" SD MET A 754 " ideal model delta sigma weight residual 112.70 122.29 -9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C TRP A 875 " pdb=" N ASN A 876 " pdb=" CA ASN A 876 " ideal model delta sigma weight residual 122.08 126.57 -4.49 1.47e+00 4.63e-01 9.35e+00 ... (remaining 11596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.26: 4890 32.26 - 64.52: 270 64.52 - 96.78: 21 96.78 - 129.03: 7 129.03 - 161.29: 1 Dihedral angle restraints: 5189 sinusoidal: 2142 harmonic: 3047 Sorted by residual: dihedral pdb=" C39 POV A1401 " pdb="C310 POV A1401 " pdb="C311 POV A1401 " pdb="C312 POV A1401 " ideal model delta sinusoidal sigma weight residual -179.51 -18.22 -161.29 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C1 NAG B 1 " pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " pdb=" C6 NAG B 1 " ideal model delta sinusoidal sigma weight residual 171.16 -75.91 -112.93 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C1 NAG B 1 " pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " pdb=" C4 NAG B 1 " ideal model delta sinusoidal sigma weight residual -64.11 48.62 -112.73 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 5186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1271 0.069 - 0.139: 94 0.139 - 0.208: 2 0.208 - 0.277: 0 0.277 - 0.347: 1 Chirality restraints: 1368 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A1202 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.80e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 5.73e-01 ... (remaining 1365 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 426 " -0.103 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO A 427 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 313 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C THR A 313 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 313 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 314 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1128 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C SER A1128 " 0.046 2.00e-02 2.50e+03 pdb=" O SER A1128 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A1129 " -0.015 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1804 2.79 - 3.32: 7403 3.32 - 3.84: 13477 3.84 - 4.37: 15364 4.37 - 4.90: 27320 Nonbonded interactions: 65368 Sorted by model distance: nonbonded pdb=" O LEU A1288 " pdb=" OG1 THR A1292 " model vdw 2.262 3.040 nonbonded pdb=" O ASP A 595 " pdb=" OG1 THR A 599 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 436 " pdb=" NE2 HIS A 578 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU A 342 " pdb=" OG SER A 402 " model vdw 2.310 3.040 nonbonded pdb=" O LEU A 710 " pdb=" NH1 ARG A 730 " model vdw 2.315 3.120 ... (remaining 65363 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 'B' selection = chain 'C' } 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: 4.010 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.003 0.158 8548 Z= 0.150 Angle : 0.570 15.403 11613 Z= 0.308 Chirality : 0.038 0.347 1368 Planarity : 0.006 0.143 1440 Dihedral : 19.055 161.292 3199 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.03 % Allowed : 21.77 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.27), residues: 1030 helix: 3.05 (0.23), residues: 536 sheet: 0.76 (0.46), residues: 118 loop : -0.26 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.030 0.002 TYR A 551 PHE 0.013 0.001 PHE A 823 TRP 0.014 0.001 TRP A 310 HIS 0.009 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8544) covalent geometry : angle 0.56012 (11601) hydrogen bonds : bond 0.16792 ( 467) hydrogen bonds : angle 5.36189 ( 1380) link_BETA1-4 : bond 0.00774 ( 2) link_BETA1-4 : angle 1.94569 ( 6) link_NAG-ASN : bond 0.01542 ( 2) link_NAG-ASN : angle 4.27092 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 TYR cc_start: 0.8656 (m-80) cc_final: 0.8392 (m-80) REVERT: A 685 MET cc_start: 0.3532 (mtt) cc_final: 0.3290 (mtp) REVERT: A 1323 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8085 (m) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.5791 time to fit residues: 65.7854 Evaluate side-chains 99 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1195 CYS Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 40.0000 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A1289 GLN A1339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107995 restraints weight = 7614.121| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.87 r_work: 0.3087 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8548 Z= 0.195 Angle : 0.658 9.366 11613 Z= 0.333 Chirality : 0.045 0.363 1368 Planarity : 0.006 0.070 1440 Dihedral : 13.085 156.147 1260 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.27 % Allowed : 18.68 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.26), residues: 1030 helix: 2.63 (0.22), residues: 544 sheet: 0.87 (0.45), residues: 115 loop : -0.38 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 344 TYR 0.012 0.002 TYR A 551 PHE 0.025 0.002 PHE A1093 TRP 0.010 0.001 TRP A1268 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8544) covalent geometry : angle 0.64950 (11601) hydrogen bonds : bond 0.09083 ( 467) hydrogen bonds : angle 4.42357 ( 1380) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 1.74873 ( 6) link_NAG-ASN : bond 0.01384 ( 2) link_NAG-ASN : angle 4.28671 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6965 (ttp80) cc_final: 0.6533 (mtm110) REVERT: A 121 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7557 (mtm110) REVERT: A 136 GLN cc_start: 0.8055 (tp40) cc_final: 0.7721 (tp-100) REVERT: A 201 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: A 203 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7244 (pt) REVERT: A 344 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: A 433 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5491 (pt) REVERT: A 685 MET cc_start: 0.4306 (OUTLIER) cc_final: 0.3676 (mmt) REVERT: A 1070 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: A 1225 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: A 1311 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7754 (mp) outliers start: 40 outliers final: 16 residues processed: 120 average time/residue: 0.6064 time to fit residues: 76.9445 Evaluate side-chains 116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 VAL Chi-restraints excluded: chain A residue 1323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A1069 GLN A1289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110374 restraints weight = 7626.027| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.90 r_work: 0.3121 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8548 Z= 0.144 Angle : 0.569 10.117 11613 Z= 0.286 Chirality : 0.041 0.342 1368 Planarity : 0.005 0.059 1440 Dihedral : 11.403 149.812 1251 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.09 % Allowed : 18.89 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.26), residues: 1030 helix: 2.76 (0.22), residues: 543 sheet: 0.87 (0.45), residues: 114 loop : -0.29 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.011 0.001 TYR A 993 PHE 0.017 0.001 PHE A1093 TRP 0.012 0.001 TRP A 310 HIS 0.002 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8544) covalent geometry : angle 0.56012 (11601) hydrogen bonds : bond 0.07697 ( 467) hydrogen bonds : angle 4.21618 ( 1380) link_BETA1-4 : bond 0.00766 ( 2) link_BETA1-4 : angle 1.47193 ( 6) link_NAG-ASN : bond 0.01327 ( 2) link_NAG-ASN : angle 4.29281 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6804 (ttp80) cc_final: 0.6570 (mtm110) REVERT: A 136 GLN cc_start: 0.8034 (tp40) cc_final: 0.7704 (tp-100) REVERT: A 203 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7168 (pt) REVERT: A 241 ARG cc_start: 0.7063 (ptp-170) cc_final: 0.6827 (ptp-170) REVERT: A 283 TYR cc_start: 0.8763 (m-80) cc_final: 0.8447 (m-80) REVERT: A 344 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7099 (mtp85) REVERT: A 685 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3665 (mmt) REVERT: A 1151 MET cc_start: 0.7734 (mmm) cc_final: 0.7489 (mmm) REVERT: A 1225 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: A 1311 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 1323 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8196 (m) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 0.6277 time to fit residues: 77.5838 Evaluate side-chains 110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 VAL Chi-restraints excluded: chain A residue 1323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 876 ASN A1053 GLN A1069 GLN A1289 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109432 restraints weight = 7810.302| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.86 r_work: 0.3110 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8548 Z= 0.152 Angle : 0.571 11.441 11613 Z= 0.289 Chirality : 0.041 0.317 1368 Planarity : 0.005 0.059 1440 Dihedral : 10.388 145.213 1248 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.42 % Allowed : 18.68 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1030 helix: 2.73 (0.22), residues: 543 sheet: 0.89 (0.45), residues: 114 loop : -0.28 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 344 TYR 0.011 0.001 TYR A 993 PHE 0.019 0.002 PHE A1093 TRP 0.011 0.001 TRP A 310 HIS 0.003 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8544) covalent geometry : angle 0.56160 (11601) hydrogen bonds : bond 0.07934 ( 467) hydrogen bonds : angle 4.15301 ( 1380) link_BETA1-4 : bond 0.00819 ( 2) link_BETA1-4 : angle 1.42490 ( 6) link_NAG-ASN : bond 0.01315 ( 2) link_NAG-ASN : angle 4.40714 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6929 (ttp80) cc_final: 0.6565 (mtm110) REVERT: A 121 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7496 (mtm110) REVERT: A 136 GLN cc_start: 0.8021 (tp40) cc_final: 0.7675 (tp-100) REVERT: A 203 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 283 TYR cc_start: 0.8778 (m-80) cc_final: 0.8447 (m-80) REVERT: A 344 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7148 (mtp85) REVERT: A 685 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3798 (mmt) REVERT: A 950 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7292 (tmtt) REVERT: A 1151 MET cc_start: 0.7728 (mmm) cc_final: 0.7477 (mmm) REVERT: A 1225 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 1311 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7750 (mp) outliers start: 32 outliers final: 13 residues processed: 120 average time/residue: 0.6234 time to fit residues: 78.9994 Evaluate side-chains 114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 876 ASN ** A1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN A1289 GLN A1339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105182 restraints weight = 7645.266| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.94 r_work: 0.3052 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8548 Z= 0.221 Angle : 0.674 11.496 11613 Z= 0.341 Chirality : 0.045 0.164 1368 Planarity : 0.006 0.060 1440 Dihedral : 9.881 151.542 1246 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.06 % Allowed : 18.14 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.26), residues: 1030 helix: 2.50 (0.22), residues: 539 sheet: 0.89 (0.45), residues: 114 loop : -0.40 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1201 TYR 0.012 0.002 TYR A 993 PHE 0.024 0.002 PHE A1093 TRP 0.011 0.002 TRP A 310 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8544) covalent geometry : angle 0.66492 (11601) hydrogen bonds : bond 0.09843 ( 467) hydrogen bonds : angle 4.34141 ( 1380) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 2.30989 ( 6) link_NAG-ASN : bond 0.00720 ( 2) link_NAG-ASN : angle 4.45959 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6556 (mtm110) REVERT: A 121 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7645 (mtm110) REVERT: A 136 GLN cc_start: 0.8015 (tp40) cc_final: 0.7654 (tp-100) REVERT: A 344 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7256 (mtp85) REVERT: A 685 MET cc_start: 0.4357 (OUTLIER) cc_final: 0.3779 (mmt) REVERT: A 950 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7310 (tmtt) REVERT: A 1070 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.4915 (mp0) REVERT: A 1151 MET cc_start: 0.7735 (mmm) cc_final: 0.7422 (mmm) REVERT: A 1162 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6970 (mmtm) REVERT: A 1311 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7747 (mp) outliers start: 38 outliers final: 21 residues processed: 124 average time/residue: 0.6419 time to fit residues: 84.1157 Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A1053 GLN A1289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108979 restraints weight = 7642.967| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.97 r_work: 0.3109 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8548 Z= 0.143 Angle : 0.552 10.599 11613 Z= 0.281 Chirality : 0.039 0.139 1368 Planarity : 0.005 0.060 1440 Dihedral : 9.088 145.440 1246 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.42 % Allowed : 19.00 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.26), residues: 1030 helix: 2.75 (0.22), residues: 543 sheet: 0.89 (0.45), residues: 114 loop : -0.29 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.011 0.001 TYR A 993 PHE 0.016 0.001 PHE A1093 TRP 0.015 0.001 TRP A 310 HIS 0.002 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8544) covalent geometry : angle 0.54035 (11601) hydrogen bonds : bond 0.07718 ( 467) hydrogen bonds : angle 4.12314 ( 1380) link_BETA1-4 : bond 0.00560 ( 2) link_BETA1-4 : angle 1.64822 ( 6) link_NAG-ASN : bond 0.00473 ( 2) link_NAG-ASN : angle 4.72065 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6435 (mtm110) REVERT: A 121 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7449 (mtm110) REVERT: A 136 GLN cc_start: 0.7974 (tp40) cc_final: 0.7613 (tp-100) REVERT: A 344 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: A 685 MET cc_start: 0.4236 (OUTLIER) cc_final: 0.3737 (mmt) REVERT: A 950 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7267 (tmtt) REVERT: A 1070 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.4941 (mp0) REVERT: A 1151 MET cc_start: 0.7663 (mmm) cc_final: 0.7416 (mmm) REVERT: A 1225 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 1311 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7728 (mp) outliers start: 32 outliers final: 17 residues processed: 120 average time/residue: 0.6677 time to fit residues: 84.4839 Evaluate side-chains 120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 0.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A1053 GLN A1289 GLN A1339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108587 restraints weight = 7672.163| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.97 r_work: 0.3101 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8548 Z= 0.150 Angle : 0.557 9.412 11613 Z= 0.285 Chirality : 0.040 0.136 1368 Planarity : 0.005 0.060 1440 Dihedral : 8.771 142.757 1244 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.42 % Allowed : 18.68 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.26), residues: 1030 helix: 2.79 (0.22), residues: 543 sheet: 0.81 (0.45), residues: 114 loop : -0.28 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.011 0.001 TYR A 993 PHE 0.019 0.001 PHE A1093 TRP 0.013 0.001 TRP A 310 HIS 0.002 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8544) covalent geometry : angle 0.54790 (11601) hydrogen bonds : bond 0.07886 ( 467) hydrogen bonds : angle 4.11662 ( 1380) link_BETA1-4 : bond 0.00515 ( 2) link_BETA1-4 : angle 1.91715 ( 6) link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 4.11146 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6476 (mtm110) REVERT: A 121 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7462 (mtm110) REVERT: A 136 GLN cc_start: 0.7977 (tp40) cc_final: 0.7616 (tp-100) REVERT: A 344 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7112 (mtp85) REVERT: A 685 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.3748 (mmt) REVERT: A 950 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7304 (tmtt) REVERT: A 1070 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.4939 (mp0) REVERT: A 1151 MET cc_start: 0.7643 (mmm) cc_final: 0.7408 (mmm) REVERT: A 1225 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: A 1311 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7747 (mp) outliers start: 32 outliers final: 16 residues processed: 118 average time/residue: 0.6940 time to fit residues: 86.2595 Evaluate side-chains 119 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN A1289 GLN A1339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115213 restraints weight = 7655.112| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.85 r_work: 0.3105 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.131 Angle : 0.522 8.088 11613 Z= 0.267 Chirality : 0.038 0.133 1368 Planarity : 0.005 0.059 1440 Dihedral : 8.519 137.320 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.88 % Allowed : 19.00 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.27), residues: 1030 helix: 2.85 (0.22), residues: 552 sheet: 0.88 (0.45), residues: 112 loop : -0.26 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.010 0.001 TYR A 312 PHE 0.016 0.001 PHE A1093 TRP 0.014 0.001 TRP A 310 HIS 0.002 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8544) covalent geometry : angle 0.51434 (11601) hydrogen bonds : bond 0.07069 ( 467) hydrogen bonds : angle 3.98919 ( 1380) link_BETA1-4 : bond 0.00502 ( 2) link_BETA1-4 : angle 2.04308 ( 6) link_NAG-ASN : bond 0.00170 ( 2) link_NAG-ASN : angle 3.53507 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6450 (mtm110) REVERT: A 121 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7409 (mtm110) REVERT: A 136 GLN cc_start: 0.8026 (tp40) cc_final: 0.7667 (tp-100) REVERT: A 344 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: A 685 MET cc_start: 0.4147 (OUTLIER) cc_final: 0.3632 (mmt) REVERT: A 950 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (tmtt) REVERT: A 1070 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.4954 (mp0) REVERT: A 1151 MET cc_start: 0.7684 (mmm) cc_final: 0.7451 (mmm) REVERT: A 1225 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7908 (m-80) outliers start: 27 outliers final: 16 residues processed: 113 average time/residue: 0.7212 time to fit residues: 85.6709 Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN A1289 GLN A1339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.192872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119107 restraints weight = 7751.891| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.18 r_work: 0.3162 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8548 Z= 0.118 Angle : 0.497 7.167 11613 Z= 0.254 Chirality : 0.038 0.132 1368 Planarity : 0.005 0.059 1440 Dihedral : 8.144 130.840 1242 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.24 % Allowed : 19.53 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.27), residues: 1030 helix: 3.00 (0.22), residues: 546 sheet: 0.85 (0.45), residues: 112 loop : -0.18 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.009 0.001 TYR A 312 PHE 0.014 0.001 PHE A1093 TRP 0.015 0.001 TRP A 310 HIS 0.002 0.000 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8544) covalent geometry : angle 0.48975 (11601) hydrogen bonds : bond 0.06288 ( 467) hydrogen bonds : angle 3.89649 ( 1380) link_BETA1-4 : bond 0.00418 ( 2) link_BETA1-4 : angle 2.08316 ( 6) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 3.04218 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6781 (ttp80) cc_final: 0.6249 (mtm110) REVERT: A 136 GLN cc_start: 0.7982 (tp40) cc_final: 0.7617 (tp-100) REVERT: A 241 ARG cc_start: 0.7059 (ptp-170) cc_final: 0.6847 (ptp-170) REVERT: A 344 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6911 (mtp85) REVERT: A 685 MET cc_start: 0.4127 (OUTLIER) cc_final: 0.3740 (mmt) REVERT: A 950 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7328 (tmtt) REVERT: A 1070 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.4932 (mp0) REVERT: A 1151 MET cc_start: 0.7585 (mmm) cc_final: 0.7351 (mmm) REVERT: A 1225 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (m-80) outliers start: 21 outliers final: 12 residues processed: 111 average time/residue: 0.6712 time to fit residues: 78.5682 Evaluate side-chains 110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1289 GLN A1339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116353 restraints weight = 7648.731| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.36 r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.134 Angle : 0.523 7.201 11613 Z= 0.268 Chirality : 0.039 0.133 1368 Planarity : 0.005 0.060 1440 Dihedral : 8.184 131.501 1242 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.35 % Allowed : 19.64 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.27), residues: 1030 helix: 2.94 (0.22), residues: 546 sheet: 0.88 (0.46), residues: 112 loop : -0.20 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.011 0.001 TYR A 993 PHE 0.018 0.001 PHE A1093 TRP 0.011 0.001 TRP A 310 HIS 0.002 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8544) covalent geometry : angle 0.51702 (11601) hydrogen bonds : bond 0.07147 ( 467) hydrogen bonds : angle 3.93875 ( 1380) link_BETA1-4 : bond 0.00524 ( 2) link_BETA1-4 : angle 2.04316 ( 6) link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 2.90818 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6367 (mtm110) REVERT: A 121 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7344 (mtm110) REVERT: A 136 GLN cc_start: 0.7990 (tp40) cc_final: 0.7618 (tp-100) REVERT: A 241 ARG cc_start: 0.7079 (ptp-170) cc_final: 0.6870 (ptp-170) REVERT: A 283 TYR cc_start: 0.8752 (m-80) cc_final: 0.8441 (m-80) REVERT: A 344 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7043 (mtp85) REVERT: A 950 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7346 (tmtt) REVERT: A 1070 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.4952 (mp0) REVERT: A 1225 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7877 (m-80) outliers start: 22 outliers final: 15 residues processed: 108 average time/residue: 0.7317 time to fit residues: 82.9223 Evaluate side-chains 112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1289 GLN A1339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.192723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116984 restraints weight = 7634.413| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.42 r_work: 0.3148 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8548 Z= 0.120 Angle : 0.504 8.056 11613 Z= 0.257 Chirality : 0.038 0.132 1368 Planarity : 0.005 0.059 1440 Dihedral : 7.978 124.923 1242 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 20.49 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.27), residues: 1030 helix: 3.03 (0.22), residues: 545 sheet: 0.93 (0.47), residues: 112 loop : -0.15 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.009 0.001 TYR A 993 PHE 0.015 0.001 PHE A1093 TRP 0.015 0.001 TRP A 310 HIS 0.002 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8544) covalent geometry : angle 0.49833 (11601) hydrogen bonds : bond 0.06451 ( 467) hydrogen bonds : angle 3.87695 ( 1380) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 2.05155 ( 6) link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 2.76444 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4453.07 seconds wall clock time: 76 minutes 20.38 seconds (4580.38 seconds total)