Starting phenix.real_space_refine on Sat Sep 12 00:46:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2026/6gtg_0065.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 91 5.49 5 Mg 4 5.21 5 S 21 5.16 5 C 7709 2.51 5 N 2100 2.21 5 O 2613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12538 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 10633 Classifications: {'peptide': 1298} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 28, 'TRANS': 1269} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 872 Classifications: {'RNAv2': 41} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 8, 'rna3p': 32} Chain: "C" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.22 Number of scatterers: 12538 At special positions: 0 Unit cell: (103.168, 131.456, 102.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 91 15.00 Mg 4 11.99 O 2613 8.00 N 2100 7.00 C 7709 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: 0.98 Conformation dependent library (CDL) restraints added in 559.0 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 38.1% alpha, 5.4% beta 18 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.980A pdb=" N ASN A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.738A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.775A pdb=" N PHE A 119 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.552A pdb=" N LYS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.732A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.555A pdb=" N LYS A 180 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.642A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.241A pdb=" N ASN A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 236 through 240 removed outlier: 4.120A pdb=" N ALA A 239 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 240' Processing helix chain 'A' and resid 265 through 272 removed outlier: 4.154A pdb=" N ASN A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.627A pdb=" N GLN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.548A pdb=" N LYS A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.299A pdb=" N VAL A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 350 through 360 removed outlier: 3.777A pdb=" N TYR A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.836A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 374 " --> pdb=" O LYS A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.514A pdb=" N GLN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.540A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.759A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA A 459 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.142A pdb=" N ILE A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 482 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.504A pdb=" N GLU A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.545A pdb=" N LEU A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.732A pdb=" N PHE A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.080A pdb=" N TYR A 585 " --> pdb=" O LYS A 581 " (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 642 through 648 removed outlier: 3.510A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.527A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.013A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.963A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 723 removed outlier: 4.513A pdb=" N ASP A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 removed outlier: 4.172A pdb=" N GLU A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 888 through 891 removed outlier: 4.362A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 895 through 907 removed outlier: 3.931A pdb=" N GLU A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 971 removed outlier: 3.759A pdb=" N SER A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 999 removed outlier: 3.877A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1016 removed outlier: 4.462A pdb=" N GLY A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.541A pdb=" N GLU A1033 " --> pdb=" O LYS A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1109 removed outlier: 3.550A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 4.115A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.538A pdb=" N LEU A1174 " --> pdb=" O PRO A1170 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.917A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1215 removed outlier: 4.456A pdb=" N THR A1208 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.626A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1266 removed outlier: 3.508A pdb=" N GLY A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1275 removed outlier: 3.519A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1297 removed outlier: 3.605A pdb=" N GLN A1296 " --> pdb=" O PHE A1292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.764A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.020A pdb=" N LYS A 823 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.772A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 655 through 661 Processing sheet with id=AA5, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.548A pdb=" N ILE A 916 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A1006 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 925 through 927 removed outlier: 3.829A pdb=" N ASP A 939 " --> pdb=" O TYR A 926 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 943 through 944 removed outlier: 3.590A pdb=" N THR A 951 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 235 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2387 1.33 - 1.45: 3612 1.45 - 1.57: 6761 1.57 - 1.69: 179 1.69 - 1.81: 33 Bond restraints: 12972 Sorted by residual: bond pdb=" C3' DG C -7 " pdb=" O3' DG C -7 " ideal model delta sigma weight residual 1.435 1.360 0.075 1.30e-02 5.92e+03 3.30e+01 bond pdb=" C3' DT C -8 " pdb=" O3' DT C -8 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.09e+01 bond pdb=" C3' DG D 0 " pdb=" O3' DG D 0 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C1' DC C -2 " pdb=" N1 DC C -2 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" C4' DT C -15 " pdb=" C3' DT C -15 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.00e-02 1.00e+04 1.25e+01 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 17307 2.85 - 5.70: 492 5.70 - 8.55: 53 8.55 - 11.40: 11 11.40 - 14.25: 1 Bond angle restraints: 17864 Sorted by residual: angle pdb=" O4' DT C -16 " pdb=" C4' DT C -16 " pdb=" C3' DT C -16 " ideal model delta sigma weight residual 106.00 102.06 3.94 6.00e-01 2.78e+00 4.30e+01 angle pdb=" O4' DA C -10 " pdb=" C4' DA C -10 " pdb=" C3' DA C -10 " ideal model delta sigma weight residual 106.00 102.09 3.91 6.00e-01 2.78e+00 4.25e+01 angle pdb=" N ILE A 575 " pdb=" CA ILE A 575 " pdb=" C ILE A 575 " ideal model delta sigma weight residual 112.29 106.36 5.93 9.40e-01 1.13e+00 3.97e+01 angle pdb=" O4' DC C -17 " pdb=" C4' DC C -17 " pdb=" C3' DC C -17 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.75e+01 angle pdb=" O4' DT C -15 " pdb=" C4' DT C -15 " pdb=" C3' DT C -15 " ideal model delta sigma weight residual 106.00 102.39 3.61 6.00e-01 2.78e+00 3.63e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6815 17.77 - 35.53: 517 35.53 - 53.30: 223 53.30 - 71.06: 67 71.06 - 88.83: 15 Dihedral angle restraints: 7637 sinusoidal: 3783 harmonic: 3854 Sorted by residual: dihedral pdb=" C4' U B -7 " pdb=" C3' U B -7 " pdb=" C2' U B -7 " pdb=" C1' U B -7 " ideal model delta sinusoidal sigma weight residual 36.34 -38.00 74.34 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' A B -18 " pdb=" C3' A B -18 " pdb=" C2' A B -18 " pdb=" C1' A B -18 " ideal model delta sinusoidal sigma weight residual 36.35 -37.26 73.61 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' U B -8 " pdb=" C3' U B -8 " pdb=" C2' U B -8 " pdb=" C1' U B -8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.04 73.39 1 3.10e+00 1.04e-01 7.13e+02 ... (remaining 7634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1440 0.068 - 0.136: 407 0.136 - 0.204: 63 0.204 - 0.272: 38 0.272 - 0.340: 12 Chirality restraints: 1960 Sorted by residual: chirality pdb=" C2' U B -17 " pdb=" C3' U B -17 " pdb=" O2' U B -17 " pdb=" C1' U B -17 " both_signs ideal model delta sigma weight residual False -2.79 -2.45 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" P A B -18 " pdb=" OP1 A B -18 " pdb=" OP2 A B -18 " pdb=" O5' A B -18 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' G B 0 " pdb=" C3' G B 0 " pdb=" O2' G B 0 " pdb=" C1' G B 0 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1957 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 178 " 0.028 2.00e-02 2.50e+03 2.08e-02 8.65e+00 pdb=" CG TYR A 178 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 178 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 178 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 178 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.42e+00 pdb=" N PRO A 670 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 225 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 226 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.040 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 181 2.62 - 3.19: 10365 3.19 - 3.76: 19620 3.76 - 4.33: 28663 4.33 - 4.90: 44599 Nonbonded interactions: 103428 Sorted by model distance: nonbonded pdb=" O2' C B 20 " pdb=" O3' A B 21 " model vdw 2.051 3.040 nonbonded pdb=" O ARG A 800 " pdb="MG MG A1401 " model vdw 2.141 2.170 nonbonded pdb=" N7 A B -12 " pdb="MG MG B 101 " model vdw 2.177 2.250 nonbonded pdb=" O PHE A 941 " pdb=" OH TYR A 984 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR A 822 " pdb=" O VAL A1051 " model vdw 2.274 3.040 ... (remaining 103423 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 12972 Z= 0.480 Angle : 1.128 14.251 17864 Z= 0.656 Chirality : 0.072 0.340 1960 Planarity : 0.007 0.073 1969 Dihedral : 16.069 88.828 5147 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.69 % Allowed : 6.57 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.96 (0.16), residues: 1296 helix: -4.71 (0.09), residues: 486 sheet: -2.84 (0.52), residues: 82 loop : -3.66 (0.18), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 202 TYR 0.050 0.004 TYR A 178 PHE 0.035 0.003 PHE A 258 TRP 0.024 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.48 (12972) covalent geometry : angle 1.12833 / 0.66 (17864) hydrogen bonds : bond 0.32018 / 20.04 ( 271) hydrogen bonds : angle 11.62287 / 7.83 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.6630 (mppt) cc_final: 0.6403 (mmtt) REVERT: A 276 SER cc_start: 0.8400 (t) cc_final: 0.8193 (p) REVERT: A 342 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.4595 (mt) REVERT: A 353 GLN cc_start: 0.7695 (tm130) cc_final: 0.7406 (tm-30) REVERT: A 394 LYS cc_start: 0.7738 (tttp) cc_final: 0.7517 (ttmt) REVERT: A 535 ASN cc_start: 0.7882 (t160) cc_final: 0.7605 (t0) REVERT: A 660 LYS cc_start: 0.5038 (tmtt) cc_final: 0.2661 (mmmm) REVERT: A 774 ILE cc_start: 0.8264 (mm) cc_final: 0.8058 (mm) REVERT: A 950 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7581 (tptt) REVERT: A 962 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7517 (mmmt) REVERT: A 972 LYS cc_start: 0.8118 (mttm) cc_final: 0.7799 (mtpt) REVERT: A 1249 ASN cc_start: 0.8382 (p0) cc_final: 0.7494 (p0) outliers start: 8 outliers final: 3 residues processed: 290 average time/residue: 0.1207 time to fit residues: 48.8187 Evaluate side-chains 183 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 148 ASN A 183 HIS A 268 ASN A 291 ASN A 481 ASN A 534 ASN A 535 ASN A 538 HIS A 638 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 HIS ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN A 952 ASN A 976 ASN A1036 ASN A1043 ASN A1056 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.186939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149337 restraints weight = 14423.711| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.36 r_work: 0.3547 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12972 Z= 0.192 Angle : 0.978 24.698 17864 Z= 0.475 Chirality : 0.084 1.259 1960 Planarity : 0.005 0.068 1969 Dihedral : 17.066 122.390 2439 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 2.07 % Allowed : 11.93 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.18), residues: 1296 helix: -3.68 (0.15), residues: 506 sheet: -2.56 (0.50), residues: 87 loop : -3.41 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 918 TYR 0.025 0.002 TYR A1130 PHE 0.020 0.002 PHE A 681 TRP 0.039 0.003 TRP A 141 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (12972) covalent geometry : angle 0.97772 / 0.48 (17864) hydrogen bonds : bond 0.08084 / 5.47 ( 271) hydrogen bonds : angle 6.79017 / 4.52 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 SER cc_start: 0.8596 (t) cc_final: 0.8370 (p) REVERT: A 353 GLN cc_start: 0.8013 (tm130) cc_final: 0.7735 (tm-30) REVERT: A 394 LYS cc_start: 0.7604 (tttp) cc_final: 0.7300 (ttmt) REVERT: A 405 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 458 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.5688 (pp) REVERT: A 640 ILE cc_start: 0.7671 (tp) cc_final: 0.7306 (pt) REVERT: A 660 LYS cc_start: 0.5291 (tmtt) cc_final: 0.2653 (mmmm) REVERT: A 853 ASN cc_start: 0.7400 (t0) cc_final: 0.7179 (t0) REVERT: A 860 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5978 (mm-30) REVERT: A 950 LYS cc_start: 0.7672 (mmmm) cc_final: 0.7446 (tptt) REVERT: A 962 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7561 (mmmt) REVERT: A 972 LYS cc_start: 0.8099 (mttm) cc_final: 0.7792 (mtpt) outliers start: 24 outliers final: 15 residues processed: 211 average time/residue: 0.1099 time to fit residues: 33.5212 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 464 ASN A 790 ASN A 853 ASN A 887 ASN ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.190608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156127 restraints weight = 14286.740| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.91 r_work: 0.3632 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12972 Z= 0.151 Angle : 0.752 17.085 17864 Z= 0.387 Chirality : 0.060 0.843 1960 Planarity : 0.004 0.055 1969 Dihedral : 16.861 145.440 2436 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 3.11 % Allowed : 12.88 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.19), residues: 1296 helix: -3.09 (0.18), residues: 513 sheet: -2.38 (0.50), residues: 87 loop : -3.18 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1166 TYR 0.037 0.002 TYR A 112 PHE 0.015 0.002 PHE A1109 TRP 0.010 0.001 TRP A 141 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (12972) covalent geometry : angle 0.75195 / 0.39 (17864) hydrogen bonds : bond 0.06850 / 4.72 ( 271) hydrogen bonds : angle 5.98480 / 3.98 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7665 (tttm) cc_final: 0.7380 (tptp) REVERT: A 214 ASN cc_start: 0.7803 (t160) cc_final: 0.7459 (m-40) REVERT: A 276 SER cc_start: 0.8578 (t) cc_final: 0.8376 (p) REVERT: A 353 GLN cc_start: 0.7943 (tm130) cc_final: 0.7529 (tm-30) REVERT: A 405 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 514 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 626 ASP cc_start: 0.7461 (t70) cc_final: 0.7042 (t70) REVERT: A 640 ILE cc_start: 0.7548 (tp) cc_final: 0.7241 (pt) REVERT: A 660 LYS cc_start: 0.5310 (tmtt) cc_final: 0.3530 (tptm) REVERT: A 962 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7726 (mmmt) REVERT: A 972 LYS cc_start: 0.8006 (mttm) cc_final: 0.7762 (mtpt) outliers start: 36 outliers final: 15 residues processed: 191 average time/residue: 0.1102 time to fit residues: 30.9748 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 683 ASN A 853 ASN ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.183435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148003 restraints weight = 14475.492| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.11 r_work: 0.3516 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12972 Z= 0.240 Angle : 0.792 15.040 17864 Z= 0.406 Chirality : 0.060 0.723 1960 Planarity : 0.005 0.070 1969 Dihedral : 16.840 138.731 2436 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 3.37 % Allowed : 14.26 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.20), residues: 1296 helix: -2.87 (0.19), residues: 521 sheet: -2.46 (0.49), residues: 90 loop : -3.13 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1298 TYR 0.037 0.003 TYR A 754 PHE 0.017 0.002 PHE A 596 TRP 0.033 0.003 TRP A 141 HIS 0.007 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (12972) covalent geometry : angle 0.79201 / 0.41 (17864) hydrogen bonds : bond 0.07129 / 5.11 ( 271) hydrogen bonds : angle 5.96916 / 3.94 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7931 (tttm) cc_final: 0.7511 (tptp) REVERT: A 276 SER cc_start: 0.8638 (t) cc_final: 0.8378 (p) REVERT: A 353 GLN cc_start: 0.8105 (tm130) cc_final: 0.7843 (tm-30) REVERT: A 405 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 485 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6528 (tp) REVERT: A 560 HIS cc_start: 0.7324 (m170) cc_final: 0.6999 (t70) REVERT: A 626 ASP cc_start: 0.7589 (t70) cc_final: 0.7117 (t70) REVERT: A 640 ILE cc_start: 0.7575 (tp) cc_final: 0.7220 (pt) REVERT: A 660 LYS cc_start: 0.5285 (tmtt) cc_final: 0.3847 (tttp) REVERT: A 932 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7862 (mmmt) REVERT: A 962 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7689 (mmmt) REVERT: A 972 LYS cc_start: 0.8220 (mttm) cc_final: 0.7926 (mtpt) outliers start: 39 outliers final: 25 residues processed: 179 average time/residue: 0.0958 time to fit residues: 25.6774 Evaluate side-chains 167 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 780 GLN ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN A1162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.186578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150640 restraints weight = 14341.386| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.03 r_work: 0.3556 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12972 Z= 0.184 Angle : 0.726 13.130 17864 Z= 0.378 Chirality : 0.056 0.606 1960 Planarity : 0.004 0.056 1969 Dihedral : 16.829 150.961 2436 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.37 % Allowed : 15.04 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.20), residues: 1296 helix: -2.67 (0.19), residues: 532 sheet: -2.43 (0.50), residues: 90 loop : -3.07 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 833 TYR 0.027 0.002 TYR A 747 PHE 0.027 0.002 PHE A 888 TRP 0.046 0.003 TRP A 141 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (12972) covalent geometry : angle 0.72616 / 0.38 (17864) hydrogen bonds : bond 0.06434 / 4.58 ( 271) hydrogen bonds : angle 5.76890 / 3.81 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7924 (tttm) cc_final: 0.7511 (tptp) REVERT: A 143 LYS cc_start: 0.6230 (tttm) cc_final: 0.5958 (tptp) REVERT: A 276 SER cc_start: 0.8620 (t) cc_final: 0.8366 (p) REVERT: A 405 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 485 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6532 (tp) REVERT: A 487 MET cc_start: 0.7150 (mmp) cc_final: 0.6449 (ptt) REVERT: A 560 HIS cc_start: 0.7256 (m170) cc_final: 0.6966 (t70) REVERT: A 626 ASP cc_start: 0.7561 (t70) cc_final: 0.7102 (t70) REVERT: A 640 ILE cc_start: 0.7567 (tp) cc_final: 0.7245 (pt) REVERT: A 660 LYS cc_start: 0.5266 (tmtt) cc_final: 0.3849 (tttp) REVERT: A 888 PHE cc_start: 0.6460 (t80) cc_final: 0.6187 (t80) REVERT: A 932 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7893 (mmmt) REVERT: A 962 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7773 (mmmt) REVERT: A 972 LYS cc_start: 0.8224 (mttm) cc_final: 0.7971 (mtpt) REVERT: A 1056 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5765 (mt0) outliers start: 39 outliers final: 28 residues processed: 176 average time/residue: 0.0940 time to fit residues: 24.9995 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN ** A1106 GLN ** 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 = 0.4245 r_free = 0.4245 target = 0.187819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152678 restraints weight = 14185.642| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.93 r_work: 0.3600 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.146 Angle : 0.683 11.824 17864 Z= 0.356 Chirality : 0.053 0.481 1960 Planarity : 0.004 0.072 1969 Dihedral : 16.681 153.324 2436 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.11 % Allowed : 15.13 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.21), residues: 1296 helix: -2.49 (0.20), residues: 527 sheet: -2.25 (0.51), residues: 90 loop : -3.00 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.025 0.002 TYR A1228 PHE 0.026 0.002 PHE A1010 TRP 0.047 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (12972) covalent geometry : angle 0.68295 / 0.36 (17864) hydrogen bonds : bond 0.05569 / 3.89 ( 271) hydrogen bonds : angle 5.54402 / 3.67 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7942 (tttm) cc_final: 0.7518 (tptp) REVERT: A 405 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 451 LEU cc_start: 0.7506 (tt) cc_final: 0.7264 (tt) REVERT: A 485 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6447 (tp) REVERT: A 487 MET cc_start: 0.7041 (mmp) cc_final: 0.6348 (ptt) REVERT: A 560 HIS cc_start: 0.7201 (m170) cc_final: 0.6973 (t70) REVERT: A 626 ASP cc_start: 0.7522 (t70) cc_final: 0.7064 (t70) REVERT: A 640 ILE cc_start: 0.7563 (tp) cc_final: 0.7261 (pt) REVERT: A 660 LYS cc_start: 0.5125 (tmtt) cc_final: 0.3757 (tttp) REVERT: A 888 PHE cc_start: 0.6340 (t80) cc_final: 0.6087 (t80) REVERT: A 932 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7882 (mmmt) REVERT: A 962 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7772 (mmmt) REVERT: A 972 LYS cc_start: 0.8127 (mttm) cc_final: 0.7917 (mtpt) outliers start: 36 outliers final: 26 residues processed: 171 average time/residue: 0.0972 time to fit residues: 24.7696 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 117 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 113 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A1106 GLN ** 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 = 0.4242 r_free = 0.4242 target = 0.188882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150865 restraints weight = 14226.929| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.14 r_work: 0.3600 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.147 Angle : 0.674 10.875 17864 Z= 0.352 Chirality : 0.052 0.394 1960 Planarity : 0.004 0.063 1969 Dihedral : 16.585 154.301 2436 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.63 % Allowed : 14.35 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.21), residues: 1296 helix: -2.37 (0.20), residues: 529 sheet: -2.05 (0.53), residues: 88 loop : -2.90 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 833 TYR 0.024 0.002 TYR A1228 PHE 0.017 0.001 PHE A1010 TRP 0.032 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (12972) covalent geometry : angle 0.67364 / 0.35 (17864) hydrogen bonds : bond 0.05629 / 3.93 ( 271) hydrogen bonds : angle 5.41743 / 3.59 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: A 96 LYS cc_start: 0.7927 (tttm) cc_final: 0.7508 (tptp) REVERT: A 214 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7508 (m-40) REVERT: A 405 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 451 LEU cc_start: 0.7463 (tt) cc_final: 0.7177 (tt) REVERT: A 485 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6445 (tp) REVERT: A 487 MET cc_start: 0.6986 (mmp) cc_final: 0.6353 (ptt) REVERT: A 560 HIS cc_start: 0.7271 (m170) cc_final: 0.6982 (t70) REVERT: A 626 ASP cc_start: 0.7519 (t70) cc_final: 0.7057 (t70) REVERT: A 640 ILE cc_start: 0.7543 (tp) cc_final: 0.7216 (pt) REVERT: A 660 LYS cc_start: 0.5071 (tmtt) cc_final: 0.3300 (tptm) REVERT: A 868 ILE cc_start: 0.6718 (mt) cc_final: 0.6516 (mt) REVERT: A 888 PHE cc_start: 0.6428 (t80) cc_final: 0.6168 (t80) REVERT: A 932 LYS cc_start: 0.8416 (mtmm) cc_final: 0.7887 (mmmt) REVERT: A 962 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7726 (mmmt) REVERT: A 972 LYS cc_start: 0.8179 (mttm) cc_final: 0.7929 (mtpt) outliers start: 42 outliers final: 32 residues processed: 180 average time/residue: 0.0961 time to fit residues: 25.8154 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 93 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 128 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.9412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN A1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.189430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151284 restraints weight = 14150.317| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.09 r_work: 0.3617 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12972 Z= 0.142 Angle : 0.660 10.050 17864 Z= 0.345 Chirality : 0.051 0.357 1960 Planarity : 0.004 0.076 1969 Dihedral : 16.547 154.448 2436 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 3.28 % Allowed : 15.47 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.21), residues: 1296 helix: -2.35 (0.20), residues: 536 sheet: -1.93 (0.54), residues: 88 loop : -2.89 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 833 TYR 0.027 0.001 TYR A1228 PHE 0.016 0.001 PHE A 362 TRP 0.028 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12972) covalent geometry : angle 0.66009 / 0.35 (17864) hydrogen bonds : bond 0.05398 / 3.72 ( 271) hydrogen bonds : angle 5.33657 / 3.54 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: A 96 LYS cc_start: 0.7893 (tttm) cc_final: 0.7500 (tptp) REVERT: A 143 LYS cc_start: 0.6184 (tttm) cc_final: 0.5962 (pttt) REVERT: A 146 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7138 (mmmt) REVERT: A 214 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7497 (m-40) REVERT: A 405 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 451 LEU cc_start: 0.7467 (tt) cc_final: 0.7216 (tt) REVERT: A 485 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6455 (tp) REVERT: A 487 MET cc_start: 0.6985 (mmp) cc_final: 0.6342 (ptt) REVERT: A 514 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 626 ASP cc_start: 0.7509 (t70) cc_final: 0.7048 (t70) REVERT: A 640 ILE cc_start: 0.7547 (tp) cc_final: 0.7258 (pt) REVERT: A 660 LYS cc_start: 0.5025 (tmtt) cc_final: 0.3364 (tptm) REVERT: A 683 ASN cc_start: 0.7177 (t0) cc_final: 0.6965 (t0) REVERT: A 868 ILE cc_start: 0.6659 (mt) cc_final: 0.6441 (mt) REVERT: A 886 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7878 (pt) REVERT: A 888 PHE cc_start: 0.6488 (t80) cc_final: 0.6236 (t80) REVERT: A 932 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7884 (mmmt) REVERT: A 962 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7763 (mmmt) REVERT: A 972 LYS cc_start: 0.8101 (mttm) cc_final: 0.7895 (mtpt) REVERT: A 1065 LYS cc_start: 0.6836 (mttt) cc_final: 0.6064 (mmmt) outliers start: 38 outliers final: 26 residues processed: 170 average time/residue: 0.0998 time to fit residues: 25.1813 Evaluate side-chains 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 384 GLN A 404 GLN A 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.187388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149271 restraints weight = 14275.711| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.14 r_work: 0.3583 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.168 Angle : 0.674 9.460 17864 Z= 0.352 Chirality : 0.052 0.358 1960 Planarity : 0.004 0.071 1969 Dihedral : 16.562 155.086 2436 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.37 % Allowed : 15.73 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.21), residues: 1296 helix: -2.29 (0.20), residues: 536 sheet: -1.91 (0.54), residues: 88 loop : -2.85 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.027 0.002 TYR A1228 PHE 0.017 0.002 PHE A 888 TRP 0.024 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (12972) covalent geometry : angle 0.67386 / 0.35 (17864) hydrogen bonds : bond 0.05488 / 3.82 ( 271) hydrogen bonds : angle 5.35627 / 3.55 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 96 LYS cc_start: 0.7951 (tttm) cc_final: 0.7530 (tptp) REVERT: A 143 LYS cc_start: 0.6229 (tttm) cc_final: 0.5967 (ptmt) REVERT: A 146 LYS cc_start: 0.7966 (mmmm) cc_final: 0.6928 (mmmm) REVERT: A 214 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7514 (m-40) REVERT: A 405 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 451 LEU cc_start: 0.7471 (tt) cc_final: 0.7246 (tt) REVERT: A 485 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6461 (tp) REVERT: A 487 MET cc_start: 0.6988 (mmp) cc_final: 0.6341 (ptt) REVERT: A 626 ASP cc_start: 0.7540 (t70) cc_final: 0.7085 (t70) REVERT: A 640 ILE cc_start: 0.7579 (tp) cc_final: 0.7300 (pt) REVERT: A 660 LYS cc_start: 0.5033 (tmtt) cc_final: 0.3350 (tptm) REVERT: A 868 ILE cc_start: 0.6714 (mt) cc_final: 0.6514 (mt) REVERT: A 932 LYS cc_start: 0.8453 (mtmm) cc_final: 0.7948 (mmmt) REVERT: A 962 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7783 (mmmt) REVERT: A 972 LYS cc_start: 0.8133 (mttm) cc_final: 0.7927 (mtpt) outliers start: 39 outliers final: 31 residues processed: 166 average time/residue: 0.1033 time to fit residues: 25.4619 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 68 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 0.0870 chunk 70 optimal weight: 9.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 353 GLN A 404 GLN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS A 934 ASN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.188408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150971 restraints weight = 14292.619| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.09 r_work: 0.3591 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.153 Angle : 0.663 8.807 17864 Z= 0.347 Chirality : 0.051 0.338 1960 Planarity : 0.004 0.069 1969 Dihedral : 16.579 155.394 2436 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.11 % Allowed : 16.25 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.21), residues: 1296 helix: -2.13 (0.21), residues: 527 sheet: -1.88 (0.54), residues: 88 loop : -2.82 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 872 TYR 0.030 0.002 TYR A 112 PHE 0.017 0.001 PHE A 362 TRP 0.024 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12972) covalent geometry : angle 0.66328 / 0.35 (17864) hydrogen bonds : bond 0.05408 / 3.75 ( 271) hydrogen bonds : angle 5.34932 / 3.54 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: A 96 LYS cc_start: 0.7973 (tttm) cc_final: 0.7541 (tptp) REVERT: A 143 LYS cc_start: 0.6204 (tttm) cc_final: 0.5939 (ptmt) REVERT: A 146 LYS cc_start: 0.7987 (mmmm) cc_final: 0.6898 (mmmm) REVERT: A 214 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: A 405 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 451 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7190 (tt) REVERT: A 485 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6411 (tp) REVERT: A 487 MET cc_start: 0.7006 (mmp) cc_final: 0.6322 (ptt) REVERT: A 567 GLU cc_start: 0.8080 (tp30) cc_final: 0.7836 (tp30) REVERT: A 626 ASP cc_start: 0.7561 (t70) cc_final: 0.7109 (t70) REVERT: A 640 ILE cc_start: 0.7562 (tp) cc_final: 0.7332 (pt) REVERT: A 660 LYS cc_start: 0.5024 (tmtt) cc_final: 0.3156 (tptm) REVERT: A 868 ILE cc_start: 0.6739 (mt) cc_final: 0.6532 (mt) REVERT: A 932 LYS cc_start: 0.8419 (mtmm) cc_final: 0.7957 (mmmt) REVERT: A 962 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7769 (mmmt) outliers start: 36 outliers final: 32 residues processed: 169 average time/residue: 0.1031 time to fit residues: 25.6199 Evaluate side-chains 179 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 47 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.187946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151821 restraints weight = 14366.976| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.12 r_work: 0.3592 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.299 12972 Z= 0.315 Angle : 1.026 59.199 17864 Z= 0.639 Chirality : 0.052 0.450 1960 Planarity : 0.005 0.087 1969 Dihedral : 16.589 155.410 2436 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.54 % Allowed : 16.08 % Favored : 80.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.21), residues: 1296 helix: -2.13 (0.21), residues: 527 sheet: -1.88 (0.54), residues: 88 loop : -2.82 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 872 TYR 0.026 0.002 TYR A 112 PHE 0.016 0.001 PHE A 362 TRP 0.021 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.32 (12972) covalent geometry : angle 1.02580 / 0.64 (17864) hydrogen bonds : bond 0.05417 / 3.75 ( 271) hydrogen bonds : angle 5.34894 / 3.54 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.68 seconds wall clock time: 45 minutes 30.32 seconds (2730.32 seconds total)