Starting phenix.real_space_refine on Wed Sep 17 20:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2025/6gtf_0064.map" } resolution = 3.63 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= 0.000 sd= 0.006 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 66 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1908 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 10871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9496 Classifications: {'peptide': 1280} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1251} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1576 Unresolved non-hydrogen dihedrals: 714 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 25, 'GLN:plan1': 16, 'PHE:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 17, 'HIS:plan': 5, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 545 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.97, per 1000 atoms: 0.27 Number of scatterers: 10871 At special positions: 0 Unit cell: (100.672, 133.12, 103.168, 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 17 16.00 P 66 15.00 O 2278 8.00 N 1908 7.00 C 6602 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: 1.27 Conformation dependent library (CDL) restraints added in 537.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 35.9% alpha, 4.1% beta 4 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.069A pdb=" N ARG A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.540A pdb=" N ILE A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.848A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.617A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.895A pdb=" N ASN A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.604A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.738A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 187 " --> pdb=" O HIS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.564A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.744A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 4.147A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.903A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.827A pdb=" N GLU A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.851A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.173A pdb=" N ALA A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.503A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.967A pdb=" N GLN A 507 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.629A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 4.346A pdb=" N ILE A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 544' Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.519A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.577A pdb=" N ASN A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.814A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.600A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.543A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 5.370A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.677A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.588A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.257A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.964A pdb=" N LEU A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.646A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 999 removed outlier: 3.847A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.593A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1110 removed outlier: 3.710A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.655A pdb=" N GLU A1175 " --> pdb=" O THR A1171 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1197 removed outlier: 4.269A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.791A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1275 removed outlier: 4.113A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A1263 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 4.525A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1295 " --> pdb=" O TYR A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 4.029A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.582A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 927 through 928 Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2010 1.32 - 1.44: 3170 1.44 - 1.57: 5874 1.57 - 1.69: 129 1.69 - 1.81: 27 Bond restraints: 11210 Sorted by residual: bond pdb=" CB TRP A 808 " pdb=" CG TRP A 808 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.17e+01 bond pdb=" CB ARG A 18 " pdb=" CG ARG A 18 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.92e+00 bond pdb=" CB PHE A 941 " pdb=" CG PHE A 941 " ideal model delta sigma weight residual 1.502 1.447 0.055 2.30e-02 1.89e+03 5.74e+00 bond pdb=" C1' DC C 4 " pdb=" N1 DC C 4 " ideal model delta sigma weight residual 1.490 1.420 0.070 3.00e-02 1.11e+03 5.44e+00 bond pdb=" CB GLN A 24 " pdb=" CG GLN A 24 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 14786 2.89 - 5.77: 428 5.77 - 8.66: 49 8.66 - 11.55: 7 11.55 - 14.44: 2 Bond angle restraints: 15272 Sorted by residual: angle pdb=" C GLN A1245 " pdb=" N ALA A1246 " pdb=" CA ALA A1246 " ideal model delta sigma weight residual 120.94 134.44 -13.50 1.90e+00 2.77e-01 5.05e+01 angle pdb=" C GLY A 892 " pdb=" N ALA A 893 " pdb=" CA ALA A 893 " ideal model delta sigma weight residual 122.35 130.65 -8.30 1.46e+00 4.69e-01 3.23e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 124.31 -10.21 2.00e+00 2.50e-01 2.61e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 110.05 104.77 5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 15267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 5650 18.78 - 37.56: 462 37.56 - 56.34: 186 56.34 - 75.11: 62 75.11 - 93.89: 12 Dihedral angle restraints: 6372 sinusoidal: 3057 harmonic: 3315 Sorted by residual: dihedral pdb=" CA ASP A1227 " pdb=" C ASP A1227 " pdb=" N TYR A1228 " pdb=" CA TYR A1228 " ideal model delta harmonic sigma weight residual 180.00 -147.66 -32.34 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA LYS A1084 " pdb=" C LYS A1084 " pdb=" N ILE A1085 " pdb=" CA ILE A1085 " ideal model delta harmonic sigma weight residual -180.00 -148.64 -31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ASP A 40 " pdb=" C ASP A 40 " pdb=" N GLU A 41 " pdb=" CA GLU A 41 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 6369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1123 0.069 - 0.138: 342 0.138 - 0.207: 52 0.207 - 0.276: 5 0.276 - 0.344: 3 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C1' U B -16 " pdb=" O4' U B -16 " pdb=" C2' U B -16 " pdb=" N1 U B -16 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 974 " pdb=" CA ILE A 974 " pdb=" CG1 ILE A 974 " pdb=" CG2 ILE A 974 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU A 914 " pdb=" CB LEU A 914 " pdb=" CD1 LEU A 914 " pdb=" CD2 LEU A 914 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1522 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 670 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1231 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A1232 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1232 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1232 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B -11 " -0.036 2.00e-02 2.50e+03 1.92e-02 8.27e+00 pdb=" N1 C B -11 " 0.042 2.00e-02 2.50e+03 pdb=" C2 C B -11 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B -11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -11 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C B -11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -11 " 0.006 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 211 2.60 - 3.18: 9059 3.18 - 3.75: 16871 3.75 - 4.33: 23040 4.33 - 4.90: 35787 Nonbonded interactions: 84968 Sorted by model distance: nonbonded pdb=" OE2 GLU A 920 " pdb=" OH TYR A1024 " model vdw 2.030 3.040 nonbonded pdb=" OE2 GLU A 594 " pdb=" N LYS A 834 " model vdw 2.101 3.120 nonbonded pdb=" N ALA A 665 " pdb=" OE2 GLU A 758 " model vdw 2.111 3.120 nonbonded pdb=" OP2 A B -18 " pdb=" N4 C B -11 " model vdw 2.121 3.120 nonbonded pdb=" NZ LYS A1221 " pdb=" OD2 ASP A1227 " model vdw 2.186 3.120 ... (remaining 84963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.870 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.010 0.106 11210 Z= 0.441 Angle : 1.173 14.437 15272 Z= 0.651 Chirality : 0.065 0.344 1525 Planarity : 0.007 0.092 1810 Dihedral : 17.174 93.892 4392 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -5.84 (0.17), residues: 1274 helix: -4.50 (0.11), residues: 458 sheet: -3.90 (0.40), residues: 106 loop : -3.52 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 833 TYR 0.046 0.004 TYR A 178 PHE 0.036 0.004 PHE A 596 TRP 0.027 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00962 (11210) covalent geometry : angle 1.17330 (15272) hydrogen bonds : bond 0.32261 ( 206) hydrogen bonds : angle 11.53947 ( 543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7950 (t80) cc_final: 0.7607 (t80) REVERT: A 118 LYS cc_start: 0.8187 (mttp) cc_final: 0.7930 (mttp) REVERT: A 246 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (pt) REVERT: A 248 TYR cc_start: 0.7795 (m-10) cc_final: 0.7426 (m-10) REVERT: A 642 ASP cc_start: 0.7619 (p0) cc_final: 0.7062 (p0) REVERT: A 667 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7394 (ttmm) REVERT: A 846 LYS cc_start: 0.9096 (mtmp) cc_final: 0.8800 (pttm) REVERT: A 859 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8601 (mmtm) REVERT: A 994 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8562 (ttmt) REVERT: A 1218 ARG cc_start: 0.7951 (ttt180) cc_final: 0.6891 (ttp80) REVERT: A 1240 PHE cc_start: 0.7605 (m-10) cc_final: 0.7187 (m-80) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.1467 time to fit residues: 41.5108 Evaluate side-chains 134 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 40.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 268 ASN A 271 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 694 HIS A 697 HIS A 759 ASN A 790 ASN A 843 HIS ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A 952 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1043 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.155672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.122161 restraints weight = 24948.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.126450 restraints weight = 11699.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.128990 restraints weight = 7200.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.130692 restraints weight = 5347.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.131690 restraints weight = 4452.279| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11210 Z= 0.140 Angle : 0.664 7.190 15272 Z= 0.365 Chirality : 0.044 0.287 1525 Planarity : 0.005 0.067 1810 Dihedral : 19.662 100.408 2208 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.37 % Allowed : 11.64 % Favored : 85.99 % 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: -4.94 (0.19), residues: 1274 helix: -3.48 (0.16), residues: 485 sheet: -3.42 (0.42), residues: 106 loop : -3.14 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.036 0.002 TYR A1099 PHE 0.013 0.002 PHE A1241 TRP 0.019 0.002 TRP A 175 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00303 (11210) covalent geometry : angle 0.66427 (15272) hydrogen bonds : bond 0.04982 ( 206) hydrogen bonds : angle 6.92280 ( 543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6411 (ttm110) cc_final: 0.5987 (ttm110) REVERT: A 108 GLN cc_start: 0.8977 (tt0) cc_final: 0.8777 (tt0) REVERT: A 116 SER cc_start: 0.8127 (t) cc_final: 0.7882 (t) REVERT: A 180 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6169 (tttt) REVERT: A 248 TYR cc_start: 0.7610 (m-10) cc_final: 0.7141 (m-10) REVERT: A 321 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.4296 (tpt) REVERT: A 846 LYS cc_start: 0.8821 (mtmp) cc_final: 0.8520 (pttm) REVERT: A 859 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8594 (mmtm) REVERT: A 1071 THR cc_start: 0.8074 (t) cc_final: 0.7713 (m) REVERT: A 1218 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7174 (ttp80) REVERT: A 1221 LYS cc_start: 0.6438 (mmtt) cc_final: 0.6088 (tptt) outliers start: 22 outliers final: 11 residues processed: 174 average time/residue: 0.1300 time to fit residues: 30.5463 Evaluate side-chains 140 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1063 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 47 optimal weight: 40.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 804 HIS A 851 ASN A 856 ASN A 887 ASN A 938 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.153104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.119357 restraints weight = 25275.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123435 restraints weight = 12272.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.125974 restraints weight = 7694.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.127644 restraints weight = 5723.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.128379 restraints weight = 4777.905| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11210 Z= 0.168 Angle : 0.643 8.917 15272 Z= 0.349 Chirality : 0.045 0.297 1525 Planarity : 0.004 0.047 1810 Dihedral : 19.442 97.640 2206 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.80 % Allowed : 13.36 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.60 (0.20), residues: 1274 helix: -3.03 (0.18), residues: 506 sheet: -3.45 (0.43), residues: 103 loop : -3.03 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.028 0.002 TYR A1099 PHE 0.022 0.002 PHE A 888 TRP 0.010 0.001 TRP A 175 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00363 (11210) covalent geometry : angle 0.64347 (15272) hydrogen bonds : bond 0.04887 ( 206) hydrogen bonds : angle 6.39681 ( 543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8753 (mtmp) cc_final: 0.8462 (pttm) REVERT: A 859 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8579 (mmtm) REVERT: A 1071 THR cc_start: 0.8290 (t) cc_final: 0.7919 (m) REVERT: A 1221 LYS cc_start: 0.6436 (mmtt) cc_final: 0.6050 (tptt) REVERT: A 1270 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8212 (mm) outliers start: 26 outliers final: 16 residues processed: 153 average time/residue: 0.1265 time to fit residues: 26.3813 Evaluate side-chains 136 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 79 optimal weight: 0.0170 chunk 48 optimal weight: 50.0000 chunk 114 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 0.1980 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN A 779 ASN A 851 ASN A 856 ASN A 922 HIS A 987 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.153696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119966 restraints weight = 25377.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.124146 restraints weight = 12227.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.126703 restraints weight = 7616.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.128408 restraints weight = 5663.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.129323 restraints weight = 4710.627| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11210 Z= 0.143 Angle : 0.601 7.146 15272 Z= 0.329 Chirality : 0.044 0.282 1525 Planarity : 0.004 0.054 1810 Dihedral : 19.269 92.892 2206 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.99 % Allowed : 14.98 % Favored : 81.03 % 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: -4.23 (0.21), residues: 1274 helix: -2.60 (0.20), residues: 504 sheet: -3.41 (0.42), residues: 104 loop : -2.90 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 948 TYR 0.027 0.002 TYR A 773 PHE 0.019 0.001 PHE A 888 TRP 0.011 0.001 TRP A 175 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00312 (11210) covalent geometry : angle 0.60093 (15272) hydrogen bonds : bond 0.04164 ( 206) hydrogen bonds : angle 5.94195 ( 543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6789 (mp0) REVERT: A 585 TYR cc_start: 0.6551 (t80) cc_final: 0.6296 (t80) REVERT: A 659 TYR cc_start: 0.7616 (t80) cc_final: 0.7384 (t80) REVERT: A 846 LYS cc_start: 0.8874 (mtmp) cc_final: 0.8551 (pttm) REVERT: A 859 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8586 (mmtm) REVERT: A 1071 THR cc_start: 0.8225 (t) cc_final: 0.7918 (m) REVERT: A 1198 GLU cc_start: 0.8405 (tp30) cc_final: 0.8199 (tp30) REVERT: A 1221 LYS cc_start: 0.6297 (mmtt) cc_final: 0.5969 (tptt) REVERT: A 1270 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8140 (mm) outliers start: 37 outliers final: 25 residues processed: 164 average time/residue: 0.1167 time to fit residues: 26.7047 Evaluate side-chains 138 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1217 MET Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 ASN A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A1036 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.150336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.115896 restraints weight = 24998.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.119902 restraints weight = 12156.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.122440 restraints weight = 7672.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123997 restraints weight = 5740.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124955 restraints weight = 4805.724| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11210 Z= 0.236 Angle : 0.695 7.928 15272 Z= 0.373 Chirality : 0.047 0.326 1525 Planarity : 0.004 0.051 1810 Dihedral : 19.292 92.730 2206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.63 % Allowed : 17.46 % 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: -4.14 (0.21), residues: 1274 helix: -2.45 (0.20), residues: 505 sheet: -3.57 (0.41), residues: 104 loop : -2.87 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 918 TYR 0.022 0.003 TYR A1099 PHE 0.020 0.002 PHE A 888 TRP 0.010 0.002 TRP A 175 HIS 0.008 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00518 (11210) covalent geometry : angle 0.69460 (15272) hydrogen bonds : bond 0.05223 ( 206) hydrogen bonds : angle 6.00581 ( 543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8173 (mmtm) REVERT: A 846 LYS cc_start: 0.8665 (mtmp) cc_final: 0.8423 (pttm) REVERT: A 1071 THR cc_start: 0.8458 (t) cc_final: 0.8130 (m) REVERT: A 1130 TYR cc_start: 0.4002 (OUTLIER) cc_final: 0.2930 (m-80) REVERT: A 1270 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8185 (mm) outliers start: 43 outliers final: 30 residues processed: 149 average time/residue: 0.1153 time to fit residues: 23.9060 Evaluate side-chains 139 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 113 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 6 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 40 optimal weight: 50.0000 overall best weight: 2.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.152644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.118072 restraints weight = 24878.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122208 restraints weight = 12009.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.124802 restraints weight = 7502.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.126492 restraints weight = 5597.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127306 restraints weight = 4680.788| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11210 Z= 0.171 Angle : 0.652 12.974 15272 Z= 0.350 Chirality : 0.045 0.291 1525 Planarity : 0.004 0.056 1810 Dihedral : 19.176 90.670 2206 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.31 % Allowed : 18.53 % Favored : 77.16 % 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: -3.92 (0.21), residues: 1274 helix: -2.17 (0.21), residues: 500 sheet: -3.34 (0.42), residues: 102 loop : -2.85 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 918 TYR 0.021 0.002 TYR A 659 PHE 0.018 0.002 PHE A 888 TRP 0.007 0.001 TRP A 175 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00377 (11210) covalent geometry : angle 0.65158 (15272) hydrogen bonds : bond 0.04314 ( 206) hydrogen bonds : angle 5.82451 ( 543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8687 (mtmp) cc_final: 0.8411 (pttm) REVERT: A 925 TYR cc_start: 0.7638 (t80) cc_final: 0.7199 (m-80) REVERT: A 1071 THR cc_start: 0.8401 (t) cc_final: 0.8094 (m) REVERT: A 1270 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8165 (mm) outliers start: 40 outliers final: 31 residues processed: 140 average time/residue: 0.1133 time to fit residues: 22.4507 Evaluate side-chains 137 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1217 MET Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 185 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 790 ASN A 802 ASN A 818 GLN A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.149206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.114664 restraints weight = 25087.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118628 restraints weight = 12361.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121158 restraints weight = 7831.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122634 restraints weight = 5881.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.123562 restraints weight = 4950.474| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11210 Z= 0.255 Angle : 0.734 16.328 15272 Z= 0.392 Chirality : 0.048 0.322 1525 Planarity : 0.004 0.056 1810 Dihedral : 19.233 92.031 2206 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.50 % Allowed : 17.78 % Favored : 76.72 % 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: -3.96 (0.21), residues: 1274 helix: -2.14 (0.21), residues: 507 sheet: -3.54 (0.42), residues: 102 loop : -2.91 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 740 TYR 0.031 0.003 TYR A1037 PHE 0.020 0.002 PHE A 888 TRP 0.008 0.001 TRP A 175 HIS 0.008 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00558 (11210) covalent geometry : angle 0.73444 (15272) hydrogen bonds : bond 0.05359 ( 206) hydrogen bonds : angle 6.01482 ( 543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8148 (mmtm) REVERT: A 846 LYS cc_start: 0.8714 (mtmp) cc_final: 0.8455 (pttm) REVERT: A 1130 TYR cc_start: 0.4028 (OUTLIER) cc_final: 0.3117 (m-80) REVERT: A 1270 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8118 (mm) outliers start: 51 outliers final: 40 residues processed: 149 average time/residue: 0.1193 time to fit residues: 24.6593 Evaluate side-chains 149 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.152648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.118214 restraints weight = 24786.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.122348 restraints weight = 11815.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.124979 restraints weight = 7392.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126634 restraints weight = 5513.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.127408 restraints weight = 4608.284| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11210 Z= 0.155 Angle : 0.645 16.613 15272 Z= 0.346 Chirality : 0.044 0.279 1525 Planarity : 0.004 0.056 1810 Dihedral : 19.082 89.199 2206 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.63 % Allowed : 18.53 % Favored : 76.83 % 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: -3.64 (0.22), residues: 1274 helix: -1.84 (0.22), residues: 502 sheet: -3.30 (0.43), residues: 102 loop : -2.76 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.030 0.002 TYR A1037 PHE 0.024 0.002 PHE A1112 TRP 0.008 0.001 TRP A 808 HIS 0.003 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00342 (11210) covalent geometry : angle 0.64536 (15272) hydrogen bonds : bond 0.04113 ( 206) hydrogen bonds : angle 5.69957 ( 543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8659 (mtmp) cc_final: 0.8421 (pttm) REVERT: A 918 ARG cc_start: 0.5623 (mmt-90) cc_final: 0.3714 (ttp-170) REVERT: A 925 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: A 1071 THR cc_start: 0.8238 (t) cc_final: 0.7797 (m) REVERT: A 1270 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8119 (mm) outliers start: 43 outliers final: 34 residues processed: 146 average time/residue: 0.1185 time to fit residues: 23.8230 Evaluate side-chains 146 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117035 restraints weight = 24695.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.121125 restraints weight = 11952.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.123603 restraints weight = 7521.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.125275 restraints weight = 5652.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.126010 restraints weight = 4725.695| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11210 Z= 0.185 Angle : 0.670 16.556 15272 Z= 0.356 Chirality : 0.045 0.297 1525 Planarity : 0.004 0.050 1810 Dihedral : 19.040 88.727 2206 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.42 % Allowed : 19.18 % Favored : 76.40 % 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: -3.55 (0.22), residues: 1274 helix: -1.75 (0.22), residues: 499 sheet: -3.27 (0.43), residues: 102 loop : -2.73 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.030 0.002 TYR A1037 PHE 0.020 0.002 PHE A 888 TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00408 (11210) covalent geometry : angle 0.66960 (15272) hydrogen bonds : bond 0.04347 ( 206) hydrogen bonds : angle 5.73768 ( 543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7021 (t80) cc_final: 0.6329 (t80) REVERT: A 846 LYS cc_start: 0.8670 (mtmp) cc_final: 0.8450 (pttm) REVERT: A 859 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8228 (tmtt) REVERT: A 918 ARG cc_start: 0.5707 (mmt-90) cc_final: 0.5432 (mmt90) REVERT: A 1071 THR cc_start: 0.8333 (t) cc_final: 0.7870 (m) REVERT: A 1217 MET cc_start: 0.5045 (mmt) cc_final: 0.4040 (mmt) REVERT: A 1270 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8098 (mm) outliers start: 41 outliers final: 36 residues processed: 145 average time/residue: 0.1260 time to fit residues: 25.4280 Evaluate side-chains 148 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 53 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 109 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A1036 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.155707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121598 restraints weight = 24534.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.125928 restraints weight = 11490.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.128636 restraints weight = 7094.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.130202 restraints weight = 5261.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.131240 restraints weight = 4414.497| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11210 Z= 0.125 Angle : 0.624 17.056 15272 Z= 0.332 Chirality : 0.043 0.259 1525 Planarity : 0.003 0.041 1810 Dihedral : 18.951 89.164 2206 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.02 % Allowed : 20.58 % Favored : 76.40 % 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: -3.21 (0.23), residues: 1274 helix: -1.50 (0.23), residues: 494 sheet: -3.01 (0.44), residues: 102 loop : -2.51 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.021 0.002 TYR A1037 PHE 0.019 0.001 PHE A 289 TRP 0.011 0.001 TRP A 808 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00275 (11210) covalent geometry : angle 0.62382 (15272) hydrogen bonds : bond 0.03621 ( 206) hydrogen bonds : angle 5.51978 ( 543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6181 (p) REVERT: A 846 LYS cc_start: 0.8571 (mtmp) cc_final: 0.8318 (pttm) REVERT: A 859 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8057 (tptt) REVERT: A 918 ARG cc_start: 0.5474 (mmt-90) cc_final: 0.3598 (ttp-170) REVERT: A 949 MET cc_start: 0.5970 (mmm) cc_final: 0.5737 (tpt) REVERT: A 1071 THR cc_start: 0.8092 (t) cc_final: 0.7670 (m) REVERT: A 1103 SER cc_start: 0.9160 (m) cc_final: 0.8902 (p) REVERT: A 1217 MET cc_start: 0.5031 (mmt) cc_final: 0.4265 (mmt) REVERT: A 1270 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8087 (mm) outliers start: 28 outliers final: 21 residues processed: 136 average time/residue: 0.1239 time to fit residues: 23.5599 Evaluate side-chains 133 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 0.0370 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 47 optimal weight: 50.0000 chunk 103 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.151485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116918 restraints weight = 24948.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.121011 restraints weight = 12044.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.123493 restraints weight = 7573.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125166 restraints weight = 5674.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.125981 restraints weight = 4762.302| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11210 Z= 0.209 Angle : 0.685 14.462 15272 Z= 0.365 Chirality : 0.046 0.304 1525 Planarity : 0.004 0.042 1810 Dihedral : 18.972 87.809 2206 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 3.88 % Allowed : 20.15 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.31 (0.23), residues: 1274 helix: -1.53 (0.23), residues: 494 sheet: -3.12 (0.44), residues: 102 loop : -2.60 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.033 0.002 TYR A1037 PHE 0.033 0.002 PHE A 941 TRP 0.007 0.001 TRP A1142 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00463 (11210) covalent geometry : angle 0.68520 (15272) hydrogen bonds : bond 0.04443 ( 206) hydrogen bonds : angle 5.63653 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.11 seconds wall clock time: 44 minutes 33.30 seconds (2673.30 seconds total)