Starting phenix.real_space_refine on Tue Jun 10 00:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtf_0064/06_2025/6gtf_0064.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtf_0064/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6gtf_0064/06_2025/6gtf_0064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtf_0064/06_2025/6gtf_0064.map" model { file = "/net/cci-nas-00/data/ceres_data/6gtf_0064/06_2025/6gtf_0064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtf_0064/06_2025/6gtf_0064.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 16, 'ARG:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 23, 'HIS:plan': 5} 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: 6.95, per 1000 atoms: 0.64 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.40 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: 3.69 Time building geometry restraints manager: 3.12 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: 1.330 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 PHE 0.036 0.004 PHE A 596 TYR 0.046 0.004 TYR A 178 ARG 0.012 0.002 ARG A 833 Details of bonding type rmsd hydrogen bonds : bond 0.32261 ( 206) hydrogen bonds : angle 11.53947 ( 543) covalent geometry : bond 0.00962 (11210) covalent geometry : angle 1.17330 (15272) *********************** 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 : 1.120 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: A 8 VAL cc_start: 0.7886 (m) cc_final: 0.7560 (m) 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: 0.7063 (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: 0.8787 (pttm) REVERT: A 859 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8602 (mmtm) 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: 0.7188 (m-80) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.3102 time to fit residues: 87.4453 Evaluate side-chains 132 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 40.0000 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 24 GLN A 268 ASN A 271 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 694 HIS A 697 HIS A 759 ASN A 804 HIS A 843 HIS A 887 ASN A 922 HIS A 942 ASN A 952 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1043 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.152947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119403 restraints weight = 24781.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.123514 restraints weight = 11823.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126045 restraints weight = 7347.446| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2533 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= 0.169 Angle : 0.690 7.451 15272 Z= 0.380 Chirality : 0.045 0.315 1525 Planarity : 0.005 0.070 1810 Dihedral : 19.742 100.096 2208 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.69 % Allowed : 11.64 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.19), residues: 1274 helix: -3.51 (0.16), residues: 487 sheet: -3.51 (0.41), residues: 106 loop : -3.17 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 175 HIS 0.004 0.001 HIS A 183 PHE 0.013 0.002 PHE A 622 TYR 0.033 0.002 TYR A1099 ARG 0.004 0.001 ARG A1053 Details of bonding type rmsd hydrogen bonds : bond 0.05577 ( 206) hydrogen bonds : angle 7.02226 ( 543) covalent geometry : bond 0.00367 (11210) covalent geometry : angle 0.68972 (15272) *********************** 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: 25 poor density : 159 time to evaluate : 1.210 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 180 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6263 (tttt) REVERT: A 248 TYR cc_start: 0.7665 (m-10) cc_final: 0.7222 (m-10) REVERT: A 321 MET cc_start: 0.4514 (tpp) cc_final: 0.4272 (tpt) REVERT: A 846 LYS cc_start: 0.8930 (mtmp) cc_final: 0.8611 (pttm) REVERT: A 859 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8679 (mmtm) REVERT: A 1071 THR cc_start: 0.8211 (t) cc_final: 0.7826 (m) REVERT: A 1218 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7190 (ttp80) REVERT: A 1221 LYS cc_start: 0.6521 (mmtt) cc_final: 0.6171 (tptt) outliers start: 25 outliers final: 12 residues processed: 171 average time/residue: 0.2825 time to fit residues: 65.1586 Evaluate side-chains 136 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 180 LYS Chi-restraints excluded: chain A residue 300 ILE 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 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 75 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 103 optimal weight: 0.0060 chunk 42 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.156897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123292 restraints weight = 25042.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.127648 restraints weight = 11739.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130460 restraints weight = 7218.952| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11210 Z= 0.119 Angle : 0.609 6.998 15272 Z= 0.332 Chirality : 0.043 0.252 1525 Planarity : 0.004 0.052 1810 Dihedral : 19.369 98.334 2206 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.05 % Allowed : 13.58 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.20), residues: 1274 helix: -2.88 (0.19), residues: 502 sheet: -3.29 (0.43), residues: 106 loop : -3.02 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.003 0.001 HIS A 697 PHE 0.021 0.001 PHE A 888 TYR 0.031 0.002 TYR A1099 ARG 0.004 0.000 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 206) hydrogen bonds : angle 6.19758 ( 543) covalent geometry : bond 0.00252 (11210) covalent geometry : angle 0.60930 (15272) *********************** 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 165 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.107 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: A 773 TYR cc_start: 0.8576 (t80) cc_final: 0.8211 (t80) REVERT: A 859 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8591 (mmtm) REVERT: A 949 MET cc_start: 0.5515 (mmm) cc_final: 0.5296 (tpt) REVERT: A 982 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7625 (mp0) REVERT: A 1071 THR cc_start: 0.7937 (t) cc_final: 0.7617 (m) REVERT: A 1111 LYS cc_start: 0.9104 (mttp) cc_final: 0.8872 (mtmt) REVERT: A 1221 LYS cc_start: 0.6313 (mmtt) cc_final: 0.5917 (tptt) REVERT: A 1250 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: A 1270 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8146 (mm) outliers start: 19 outliers final: 8 residues processed: 160 average time/residue: 0.2617 time to fit residues: 57.4088 Evaluate side-chains 137 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 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 1176 LYS Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A 987 GLN A1036 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.150777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.116760 restraints weight = 25322.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120809 restraints weight = 12327.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123310 restraints weight = 7750.303| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11210 Z= 0.208 Angle : 0.672 7.059 15272 Z= 0.364 Chirality : 0.046 0.320 1525 Planarity : 0.004 0.058 1810 Dihedral : 19.364 92.851 2206 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 3.66 % Allowed : 14.66 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.21), residues: 1274 helix: -2.58 (0.20), residues: 506 sheet: -3.30 (0.43), residues: 105 loop : -2.97 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1142 HIS 0.008 0.001 HIS A 183 PHE 0.020 0.002 PHE A 888 TYR 0.028 0.002 TYR A 248 ARG 0.005 0.001 ARG A 948 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 206) hydrogen bonds : angle 6.16558 ( 543) covalent geometry : bond 0.00452 (11210) covalent geometry : angle 0.67215 (15272) *********************** 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 169 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.114 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: 0.6883 (t80) cc_final: 0.6220 (t80) REVERT: A 265 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6970 (mt-10) REVERT: A 596 PHE cc_start: 0.7286 (p90) cc_final: 0.6895 (p90) REVERT: A 846 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8461 (pttm) REVERT: A 859 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8596 (mmtm) REVERT: A 979 GLU cc_start: 0.7802 (pm20) cc_final: 0.7578 (pm20) REVERT: A 981 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7932 (mmtp) REVERT: A 982 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7813 (mp0) REVERT: A 1071 THR cc_start: 0.8213 (t) cc_final: 0.7893 (m) REVERT: A 1229 LEU cc_start: 0.8547 (mt) cc_final: 0.8344 (mm) REVERT: A 1270 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8144 (mm) outliers start: 34 outliers final: 22 residues processed: 158 average time/residue: 0.2535 time to fit residues: 55.6477 Evaluate side-chains 146 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 300 ILE Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 661 LEU 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 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN 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 1063 THR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1219 ASN 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 5 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 56 optimal weight: 0.0770 chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.152654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118950 restraints weight = 24941.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123012 restraints weight = 12134.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.125611 restraints weight = 7601.080| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3718 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= 0.151 Angle : 0.611 7.245 15272 Z= 0.331 Chirality : 0.044 0.285 1525 Planarity : 0.004 0.052 1810 Dihedral : 19.197 89.311 2206 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.66 % Allowed : 16.70 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.21), residues: 1274 helix: -2.24 (0.21), residues: 501 sheet: -3.23 (0.42), residues: 106 loop : -2.83 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.005 0.001 HIS A 183 PHE 0.016 0.001 PHE A 888 TYR 0.030 0.002 TYR A 773 ARG 0.003 0.000 ARG A1053 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 206) hydrogen bonds : angle 5.84968 ( 543) covalent geometry : bond 0.00331 (11210) covalent geometry : angle 0.61095 (15272) *********************** 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 156 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.286 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 178 TYR cc_start: 0.6781 (t80) cc_final: 0.6198 (t80) REVERT: A 596 PHE cc_start: 0.7067 (p90) cc_final: 0.6802 (p90) REVERT: A 675 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.6367 (p) REVERT: A 846 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8378 (pttm) REVERT: A 859 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8599 (mmtm) REVERT: A 918 ARG cc_start: 0.5579 (mmt-90) cc_final: 0.5227 (mmt90) REVERT: A 982 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7791 (mp0) REVERT: A 1071 THR cc_start: 0.8181 (t) cc_final: 0.7881 (m) REVERT: A 1130 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.2727 (m-80) REVERT: A 1198 GLU cc_start: 0.8379 (tp30) cc_final: 0.8169 (tp30) REVERT: A 1217 MET cc_start: 0.4161 (mmt) cc_final: 0.3760 (mmt) REVERT: A 1270 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8167 (mm) outliers start: 34 outliers final: 19 residues processed: 146 average time/residue: 0.2894 time to fit residues: 59.5317 Evaluate side-chains 130 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 661 LEU Chi-restraints excluded: chain A residue 675 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 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 1051 VAL 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 1219 ASN 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 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.148161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.114009 restraints weight = 25367.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117796 restraints weight = 12662.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.120250 restraints weight = 8111.686| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11210 Z= 0.296 Angle : 0.775 10.980 15272 Z= 0.414 Chirality : 0.050 0.346 1525 Planarity : 0.005 0.057 1810 Dihedral : 19.361 92.878 2206 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 4.31 % Allowed : 17.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.21), residues: 1274 helix: -2.24 (0.21), residues: 495 sheet: -3.56 (0.40), residues: 107 loop : -2.91 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1142 HIS 0.009 0.002 HIS A 183 PHE 0.024 0.003 PHE A 941 TYR 0.028 0.003 TYR A 773 ARG 0.004 0.001 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.05840 ( 206) hydrogen bonds : angle 6.27085 ( 543) covalent geometry : bond 0.00648 (11210) covalent geometry : angle 0.77473 (15272) *********************** 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 157 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.249 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: A 107 LYS cc_start: 0.8813 (tptp) cc_final: 0.8606 (tppt) REVERT: A 265 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6945 (mt-10) REVERT: A 719 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8172 (mmtm) REVERT: A 859 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8567 (tmtt) REVERT: A 1130 TYR cc_start: 0.4001 (OUTLIER) cc_final: 0.3103 (m-80) REVERT: A 1198 GLU cc_start: 0.8420 (tp30) cc_final: 0.7902 (tm-30) REVERT: A 1250 MET cc_start: 0.8511 (mmm) cc_final: 0.8144 (mmm) REVERT: A 1270 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8083 (mm) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.2587 time to fit residues: 53.8293 Evaluate side-chains 139 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU 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 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 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN 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 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 1219 ASN 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 65 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.151412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.116924 restraints weight = 25132.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.120967 restraints weight = 12164.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.123589 restraints weight = 7631.131| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11210 Z= 0.183 Angle : 0.670 14.040 15272 Z= 0.361 Chirality : 0.046 0.298 1525 Planarity : 0.004 0.062 1810 Dihedral : 19.182 90.986 2206 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.56 % Allowed : 20.37 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.22), residues: 1274 helix: -1.96 (0.22), residues: 499 sheet: -3.30 (0.42), residues: 106 loop : -2.82 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 808 HIS 0.003 0.001 HIS A 697 PHE 0.018 0.002 PHE A1112 TYR 0.031 0.002 TYR A 773 ARG 0.003 0.001 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 206) hydrogen bonds : angle 5.96923 ( 543) covalent geometry : bond 0.00405 (11210) covalent geometry : angle 0.67037 (15272) *********************** 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 145 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.123 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 178 TYR cc_start: 0.6960 (t80) cc_final: 0.6300 (t80) REVERT: A 719 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8190 (mmtm) REVERT: A 918 ARG cc_start: 0.5661 (mmt-90) cc_final: 0.3744 (ttp-170) REVERT: A 1071 THR cc_start: 0.8247 (t) cc_final: 0.7758 (m) REVERT: A 1250 MET cc_start: 0.8459 (mmm) cc_final: 0.8090 (mmm) REVERT: A 1270 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8207 (mm) outliers start: 33 outliers final: 27 residues processed: 138 average time/residue: 0.2562 time to fit residues: 49.6248 Evaluate side-chains 133 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 642 ASP Chi-restraints excluded: chain A residue 661 LEU 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 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1008 LEU 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 1185 TYR Chi-restraints excluded: chain A residue 1219 ASN 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 21 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1219 ASN A1300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.150401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.115980 restraints weight = 24857.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120069 restraints weight = 12102.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.122603 restraints weight = 7612.284| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11210 Z= 0.209 Angle : 0.686 14.766 15272 Z= 0.368 Chirality : 0.046 0.306 1525 Planarity : 0.004 0.056 1810 Dihedral : 19.136 90.610 2206 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 4.09 % Allowed : 20.04 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.22), residues: 1274 helix: -1.89 (0.22), residues: 501 sheet: -3.32 (0.42), residues: 105 loop : -2.85 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 175 HIS 0.004 0.001 HIS A 731 PHE 0.016 0.002 PHE A 289 TYR 0.028 0.002 TYR A 773 ARG 0.004 0.001 ARG A 921 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 206) hydrogen bonds : angle 5.92411 ( 543) covalent geometry : bond 0.00458 (11210) covalent geometry : angle 0.68602 (15272) *********************** 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 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.193 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 178 TYR cc_start: 0.6996 (t80) cc_final: 0.6329 (t80) REVERT: A 846 LYS cc_start: 0.8599 (pttm) cc_final: 0.8336 (ptpt) REVERT: A 859 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8198 (tmtt) REVERT: A 918 ARG cc_start: 0.5671 (mmt-90) cc_final: 0.3660 (ttp-170) REVERT: A 1071 THR cc_start: 0.8161 (t) cc_final: 0.7691 (m) REVERT: A 1250 MET cc_start: 0.8500 (mmm) cc_final: 0.8098 (mmm) REVERT: A 1270 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8132 (mm) outliers start: 38 outliers final: 34 residues processed: 136 average time/residue: 0.2678 time to fit residues: 50.4626 Evaluate side-chains 139 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 329 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 675 SER Chi-restraints excluded: chain A residue 788 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 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN 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 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU 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 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1219 ASN 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 6 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 39 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 50.0000 chunk 21 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 790 ASN A 816 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.151927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117564 restraints weight = 24979.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.121664 restraints weight = 12054.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.124292 restraints weight = 7541.674| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11210 Z= 0.168 Angle : 0.647 15.420 15272 Z= 0.348 Chirality : 0.044 0.287 1525 Planarity : 0.004 0.045 1810 Dihedral : 19.073 88.762 2206 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.53 % Allowed : 19.61 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.22), residues: 1274 helix: -1.74 (0.23), residues: 490 sheet: -3.26 (0.42), residues: 105 loop : -2.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 175 HIS 0.003 0.001 HIS A 697 PHE 0.017 0.002 PHE A 289 TYR 0.030 0.002 TYR A 773 ARG 0.003 0.000 ARG A 921 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 206) hydrogen bonds : angle 5.77031 ( 543) covalent geometry : bond 0.00371 (11210) covalent geometry : angle 0.64722 (15272) *********************** 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 150 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 1.171 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 846 LYS cc_start: 0.8545 (pttm) cc_final: 0.8324 (ptpt) REVERT: A 859 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8224 (tmtt) REVERT: A 918 ARG cc_start: 0.5682 (mmt-90) cc_final: 0.3651 (ttp-170) REVERT: A 1071 THR cc_start: 0.8144 (t) cc_final: 0.7686 (m) REVERT: A 1250 MET cc_start: 0.8461 (mmm) cc_final: 0.8033 (mmm) REVERT: A 1270 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (mm) outliers start: 42 outliers final: 38 residues processed: 141 average time/residue: 0.2964 time to fit residues: 57.7237 Evaluate side-chains 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 329 LEU 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 667 LYS 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 859 LYS 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 938 GLN 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 1035 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 1219 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1240 PHE 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 85 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.148167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.113915 restraints weight = 25153.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117800 restraints weight = 12546.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120167 restraints weight = 8008.954| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11210 Z= 0.284 Angle : 0.760 15.610 15272 Z= 0.407 Chirality : 0.049 0.331 1525 Planarity : 0.005 0.053 1810 Dihedral : 19.185 89.198 2206 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.42 % Allowed : 19.83 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.22), residues: 1274 helix: -1.87 (0.22), residues: 489 sheet: -3.46 (0.41), residues: 105 loop : -2.88 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 175 HIS 0.006 0.002 HIS A 731 PHE 0.022 0.003 PHE A 941 TYR 0.030 0.003 TYR A 773 ARG 0.003 0.001 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 206) hydrogen bonds : angle 6.10756 ( 543) covalent geometry : bond 0.00620 (11210) covalent geometry : angle 0.76026 (15272) ********************** 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 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.162 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: A 141 TRP cc_start: 0.7718 (t60) cc_final: 0.7194 (t60) REVERT: A 265 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6838 (mt-10) REVERT: A 719 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8195 (mmtm) REVERT: A 1071 THR cc_start: 0.8337 (t) cc_final: 0.7867 (m) REVERT: A 1217 MET cc_start: 0.4127 (mmt) cc_final: 0.3398 (mmt) REVERT: A 1270 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8053 (mm) outliers start: 41 outliers final: 37 residues processed: 141 average time/residue: 0.2785 time to fit residues: 54.6228 Evaluate side-chains 144 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 131 LYS 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 603 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 788 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 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN 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 1035 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 1219 ASN Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1240 PHE 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 18 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.149119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.114924 restraints weight = 25230.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.118892 restraints weight = 12457.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121130 restraints weight = 7902.586| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11210 Z= 0.238 Angle : 0.728 15.726 15272 Z= 0.388 Chirality : 0.047 0.319 1525 Planarity : 0.004 0.060 1810 Dihedral : 19.162 89.092 2206 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 4.20 % Allowed : 20.04 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.22), residues: 1274 helix: -1.78 (0.22), residues: 489 sheet: -3.44 (0.41), residues: 105 loop : -2.86 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 175 HIS 0.005 0.001 HIS A 731 PHE 0.016 0.002 PHE A 289 TYR 0.029 0.002 TYR A 773 ARG 0.003 0.001 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 206) hydrogen bonds : angle 6.03012 ( 543) covalent geometry : bond 0.00522 (11210) covalent geometry : angle 0.72795 (15272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4596.18 seconds wall clock time: 80 minutes 52.99 seconds (4852.99 seconds total)