Starting phenix.real_space_refine on Thu Sep 18 00:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtg_0065/09_2025/6gtg_0065.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtg_0065/09_2025/6gtg_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_2025/6gtg_0065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2025/6gtg_0065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2025/6gtg_0065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtg_0065/09_2025/6gtg_0065.map" } 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-2.0-5805/lib/python3.9/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: {'RNA': 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: 3.27, per 1000 atoms: 0.26 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: 1.07 Conformation dependent library (CDL) restraints added in 573.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.84 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: 2.69 Time building geometry restraints manager: 1.43 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=" C LEU A 669 " pdb=" N PRO A 670 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" C ILE A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.42e+00 bond pdb=" CB ASP A 917 " pdb=" CG ASP A 917 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.40e+00 bond pdb=" CB ASP A1046 " pdb=" CG ASP A1046 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.21e+00 bond pdb=" CD LYS A 981 " pdb=" CE LYS A 981 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.44e+00 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 17393 2.85 - 5.70: 412 5.70 - 8.55: 47 8.55 - 11.40: 11 11.40 - 14.25: 1 Bond angle restraints: 17864 Sorted by residual: 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=" C LEU A1151 " pdb=" N ILE A1152 " pdb=" CA ILE A1152 " ideal model delta sigma weight residual 121.97 131.45 -9.48 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C PHE A1045 " pdb=" N ASP A1046 " pdb=" CA ASP A1046 " ideal model delta sigma weight residual 124.82 134.07 -9.25 1.78e+00 3.16e-01 2.70e+01 angle pdb=" N VAL A 821 " pdb=" CA VAL A 821 " pdb=" C VAL A 821 " ideal model delta sigma weight residual 112.96 107.89 5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N ILE A 728 " pdb=" CA ILE A 728 " pdb=" C ILE A 728 " ideal model delta sigma weight residual 113.39 106.99 6.40 1.47e+00 4.63e-01 1.89e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6940 17.77 - 35.53: 514 35.53 - 53.30: 213 53.30 - 71.06: 79 71.06 - 88.83: 15 Dihedral angle restraints: 7761 sinusoidal: 3907 harmonic: 3854 Sorted by residual: dihedral pdb=" CA ASP A 313 " pdb=" C ASP A 313 " pdb=" N LYS A 314 " pdb=" CA LYS A 314 " ideal model delta harmonic sigma weight residual -180.00 -147.48 -32.52 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LYS A1047 " pdb=" C LYS A1047 " pdb=" N THR A1048 " pdb=" CA THR A1048 " ideal model delta harmonic sigma weight residual -180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU A 537 " pdb=" C LEU A 537 " pdb=" N HIS A 538 " pdb=" CA HIS A 538 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1282 0.052 - 0.104: 546 0.104 - 0.155: 108 0.155 - 0.207: 18 0.207 - 0.259: 6 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CB ILE A 545 " pdb=" CA ILE A 545 " pdb=" CG1 ILE A 545 " pdb=" CG2 ILE A 545 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A1008 " pdb=" CB LEU A1008 " pdb=" CD1 LEU A1008 " pdb=" CD2 LEU A1008 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE A1191 " pdb=" CA ILE A1191 " pdb=" CG1 ILE A1191 " pdb=" CG2 ILE A1191 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+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: 1.000 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.120 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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= 0.374 Angle : 1.069 14.251 17864 Z= 0.579 Chirality : 0.058 0.259 1960 Planarity : 0.007 0.073 1969 Dihedral : 16.101 88.828 5271 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 aren 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 covalent geometry : bond 0.00861 (12972) covalent geometry : angle 1.06937 (17864) hydrogen bonds : bond 0.32018 ( 271) hydrogen bonds : angle 11.62287 ( 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 : 0.430 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: 0.7739 (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: 0.1381 time to fit residues: 55.2354 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 : 0.464 ------------------------------------------------------------------------------- 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: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 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: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 183 HIS A 268 ASN A 291 ASN A 464 ASN A 534 ASN A 535 ASN A 538 HIS A 638 ASN A 780 GLN A 790 ASN A 887 ASN A 952 ASN A 976 ASN A1043 ASN A1056 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.189199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154388 restraints weight = 14264.959| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.01 r_work: 0.3590 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12972 Z= 0.149 Angle : 0.650 9.111 17864 Z= 0.360 Chirality : 0.041 0.192 1960 Planarity : 0.005 0.067 1969 Dihedral : 17.884 87.335 2563 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.59 % Allowed : 11.93 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.03 (0.18), residues: 1296 helix: -3.56 (0.16), residues: 508 sheet: -2.48 (0.50), residues: 87 loop : -3.35 (0.20), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 918 TYR 0.018 0.002 TYR A 659 PHE 0.021 0.002 PHE A 681 TRP 0.031 0.002 TRP A 141 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00327 (12972) covalent geometry : angle 0.65009 (17864) hydrogen bonds : bond 0.06395 ( 271) hydrogen bonds : angle 6.31326 ( 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 221 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.6473 (mppt) cc_final: 0.6245 (mmtm) REVERT: A 276 SER cc_start: 0.8606 (t) cc_final: 0.8370 (p) REVERT: A 353 GLN cc_start: 0.7947 (tm130) cc_final: 0.7710 (tm-30) REVERT: A 394 LYS cc_start: 0.7555 (tttp) cc_final: 0.7241 (ttmt) REVERT: A 405 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 458 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.5393 (pp) REVERT: A 514 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8214 (mt) REVERT: A 626 ASP cc_start: 0.7556 (t70) cc_final: 0.7099 (t70) REVERT: A 640 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7262 (pt) REVERT: A 660 LYS cc_start: 0.5345 (tmtt) cc_final: 0.3604 (tttt) REVERT: A 962 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7758 (mmmt) REVERT: A 972 LYS cc_start: 0.8086 (mttm) cc_final: 0.7851 (mtpt) REVERT: A 1014 ARG cc_start: 0.6100 (ptp-170) cc_final: 0.5744 (ptp-170) REVERT: A 1065 LYS cc_start: 0.6843 (mttt) cc_final: 0.6119 (mmmt) outliers start: 30 outliers final: 16 residues processed: 214 average time/residue: 0.1227 time to fit residues: 37.5629 Evaluate side-chains 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 97 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 376 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 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 640 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 1264 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 125 GLN A 271 ASN A 464 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 HIS ** 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 = 0.4187 r_free = 0.4187 target = 0.182988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145753 restraints weight = 14561.634| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.28 r_work: 0.3494 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12972 Z= 0.206 Angle : 0.652 9.524 17864 Z= 0.358 Chirality : 0.043 0.185 1960 Planarity : 0.004 0.065 1969 Dihedral : 17.829 87.751 2562 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 3.28 % Allowed : 13.48 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.19), residues: 1296 helix: -3.09 (0.18), residues: 525 sheet: -2.43 (0.49), residues: 90 loop : -3.22 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 833 TYR 0.024 0.002 TYR A1228 PHE 0.017 0.002 PHE A 596 TRP 0.015 0.002 TRP A 141 HIS 0.008 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00470 (12972) covalent geometry : angle 0.65212 (17864) hydrogen bonds : bond 0.05939 ( 271) hydrogen bonds : angle 5.84404 ( 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 210 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 SER cc_start: 0.8657 (t) cc_final: 0.8415 (p) REVERT: A 342 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5426 (pp) REVERT: A 394 LYS cc_start: 0.7559 (tttp) cc_final: 0.7228 (ttmt) REVERT: A 395 ASN cc_start: 0.7737 (t0) cc_final: 0.7477 (t0) REVERT: A 485 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6595 (tp) REVERT: A 487 MET cc_start: 0.7157 (mmp) cc_final: 0.6400 (ptt) REVERT: A 626 ASP cc_start: 0.7598 (t70) cc_final: 0.7149 (t70) REVERT: A 640 ILE cc_start: 0.7619 (tp) cc_final: 0.7271 (pt) REVERT: A 660 LYS cc_start: 0.5356 (tmtt) cc_final: 0.3855 (tttm) REVERT: A 770 SER cc_start: 0.7074 (OUTLIER) cc_final: 0.6791 (m) REVERT: A 962 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7817 (mmmt) REVERT: A 972 LYS cc_start: 0.8183 (mttm) cc_final: 0.7949 (mtpt) outliers start: 38 outliers final: 23 residues processed: 199 average time/residue: 0.1113 time to fit residues: 32.6004 Evaluate side-chains 177 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 266 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 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 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 770 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.0000 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.189703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152080 restraints weight = 14272.534| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.02 r_work: 0.3625 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12972 Z= 0.118 Angle : 0.571 8.905 17864 Z= 0.315 Chirality : 0.039 0.172 1960 Planarity : 0.004 0.065 1969 Dihedral : 17.328 85.773 2562 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.77 % Allowed : 13.66 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.20), residues: 1296 helix: -2.60 (0.20), residues: 513 sheet: -2.32 (0.49), residues: 90 loop : -3.02 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1014 TYR 0.038 0.002 TYR A 112 PHE 0.013 0.001 PHE A 362 TRP 0.030 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00255 (12972) covalent geometry : angle 0.57148 (17864) hydrogen bonds : bond 0.04493 ( 271) hydrogen bonds : angle 5.29853 ( 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 204 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: A 43 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7310 (ttp-110) REVERT: A 214 ASN cc_start: 0.7785 (t160) cc_final: 0.7536 (m-40) REVERT: A 342 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.4683 (mt) REVERT: A 394 LYS cc_start: 0.7401 (tttp) cc_final: 0.7030 (ttpt) REVERT: A 485 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6449 (tp) REVERT: A 487 MET cc_start: 0.6989 (mmp) cc_final: 0.6279 (ptt) REVERT: A 560 HIS cc_start: 0.7318 (m-70) cc_final: 0.6909 (t70) REVERT: A 626 ASP cc_start: 0.7512 (t70) cc_final: 0.7062 (t70) REVERT: A 640 ILE cc_start: 0.7509 (tp) cc_final: 0.7128 (pt) REVERT: A 660 LYS cc_start: 0.5184 (tmtt) cc_final: 0.3273 (tptm) REVERT: A 932 LYS cc_start: 0.8460 (mtmm) cc_final: 0.7920 (mmmt) REVERT: A 939 ASP cc_start: 0.6649 (m-30) cc_final: 0.6446 (m-30) REVERT: A 962 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7826 (mmmt) REVERT: A 1010 PHE cc_start: 0.6110 (t80) cc_final: 0.5805 (t80) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.1156 time to fit residues: 32.4810 Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 67 SER 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 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1130 TYR 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: 0.0170 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 271 ASN A1056 GLN A1162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152528 restraints weight = 14268.487| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.19 r_work: 0.3610 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12972 Z= 0.120 Angle : 0.553 6.872 17864 Z= 0.305 Chirality : 0.039 0.172 1960 Planarity : 0.004 0.066 1969 Dihedral : 17.187 81.212 2562 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.68 % Allowed : 14.69 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.21), residues: 1296 helix: -2.21 (0.21), residues: 509 sheet: -2.04 (0.52), residues: 88 loop : -2.85 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1014 TYR 0.023 0.001 TYR A 112 PHE 0.015 0.001 PHE A 888 TRP 0.044 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00263 (12972) covalent geometry : angle 0.55333 (17864) hydrogen bonds : bond 0.04467 ( 271) hydrogen bonds : angle 5.10126 ( 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 187 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7805 (t160) cc_final: 0.7558 (m-40) REVERT: A 394 LYS cc_start: 0.7340 (tttp) cc_final: 0.6892 (ttpt) REVERT: A 485 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6329 (tp) REVERT: A 487 MET cc_start: 0.7005 (mmp) cc_final: 0.6285 (ptt) REVERT: A 560 HIS cc_start: 0.7349 (m-70) cc_final: 0.6990 (t70) REVERT: A 626 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7130 (t70) REVERT: A 640 ILE cc_start: 0.7426 (tp) cc_final: 0.7206 (pt) REVERT: A 660 LYS cc_start: 0.5161 (tmtt) cc_final: 0.3459 (tptm) REVERT: A 888 PHE cc_start: 0.5828 (t80) cc_final: 0.5291 (t80) REVERT: A 932 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8066 (mmmt) REVERT: A 939 ASP cc_start: 0.6690 (m-30) cc_final: 0.6448 (m-30) REVERT: A 962 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7792 (mmmt) REVERT: A 1010 PHE cc_start: 0.5940 (t80) cc_final: 0.5707 (t80) outliers start: 31 outliers final: 23 residues processed: 174 average time/residue: 0.1136 time to fit residues: 28.8807 Evaluate side-chains 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 503 SER 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 626 ASP Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1003 VAL 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: 0.0870 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN A1118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159932 restraints weight = 14066.943| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.71 r_work: 0.3687 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12972 Z= 0.109 Angle : 0.530 6.278 17864 Z= 0.294 Chirality : 0.038 0.219 1960 Planarity : 0.004 0.066 1969 Dihedral : 17.074 79.622 2562 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.94 % Allowed : 14.52 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.22), residues: 1296 helix: -2.04 (0.21), residues: 515 sheet: -1.84 (0.53), residues: 88 loop : -2.75 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1014 TYR 0.021 0.001 TYR A1228 PHE 0.012 0.001 PHE A 888 TRP 0.028 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00236 (12972) covalent geometry : angle 0.53039 (17864) hydrogen bonds : bond 0.04303 ( 271) hydrogen bonds : angle 4.94478 ( 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 190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7701 (tttt) cc_final: 0.7450 (tptp) REVERT: A 394 LYS cc_start: 0.7273 (tttp) cc_final: 0.6898 (ttmt) REVERT: A 485 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6519 (tp) REVERT: A 487 MET cc_start: 0.6840 (mmp) cc_final: 0.6364 (ptt) REVERT: A 626 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7067 (t70) REVERT: A 640 ILE cc_start: 0.7415 (tp) cc_final: 0.6990 (pt) REVERT: A 660 LYS cc_start: 0.5223 (tmtt) cc_final: 0.3525 (tptm) REVERT: A 888 PHE cc_start: 0.5814 (t80) cc_final: 0.5358 (t80) REVERT: A 939 ASP cc_start: 0.6576 (m-30) cc_final: 0.6305 (m-30) REVERT: A 962 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7918 (mmmt) REVERT: A 1010 PHE cc_start: 0.5855 (t80) cc_final: 0.5630 (t80) REVERT: A 1065 LYS cc_start: 0.6772 (mttt) cc_final: 0.6063 (mmmt) outliers start: 34 outliers final: 21 residues processed: 177 average time/residue: 0.1204 time to fit residues: 30.7960 Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 290 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 710 PHE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1003 VAL 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: 20.0000 chunk 112 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN A 599 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 ASN A1153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146810 restraints weight = 14236.294| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.16 r_work: 0.3533 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12972 Z= 0.201 Angle : 0.613 7.756 17864 Z= 0.335 Chirality : 0.042 0.194 1960 Planarity : 0.004 0.068 1969 Dihedral : 17.344 82.073 2562 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.28 % Allowed : 15.73 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.22), residues: 1296 helix: -2.03 (0.22), residues: 522 sheet: -1.95 (0.52), residues: 88 loop : -2.72 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 833 TYR 0.021 0.002 TYR A1228 PHE 0.026 0.002 PHE A 888 TRP 0.031 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00460 (12972) covalent geometry : angle 0.61256 (17864) hydrogen bonds : bond 0.05135 ( 271) hydrogen bonds : angle 5.22062 ( 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 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8036 (tttt) cc_final: 0.7513 (tptp) REVERT: A 394 LYS cc_start: 0.7406 (tttp) cc_final: 0.6946 (ttpt) REVERT: A 485 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6347 (tp) REVERT: A 487 MET cc_start: 0.6915 (mmp) cc_final: 0.6335 (ptt) REVERT: A 626 ASP cc_start: 0.7623 (t70) cc_final: 0.7146 (t70) REVERT: A 640 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6888 (pt) REVERT: A 660 LYS cc_start: 0.4971 (tmtt) cc_final: 0.3392 (tptp) REVERT: A 939 ASP cc_start: 0.7083 (m-30) cc_final: 0.6789 (m-30) REVERT: A 962 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7802 (mmmt) outliers start: 38 outliers final: 30 residues processed: 165 average time/residue: 0.1103 time to fit residues: 27.0669 Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 260 LEU 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 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 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 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 640 ILE Chi-restraints excluded: chain A residue 900 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 940 THR 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: 5.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 790 ASN A 901 ASN A1070 GLN A1118 ASN 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 = 0.189951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154534 restraints weight = 14195.279| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.81 r_work: 0.3610 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12972 Z= 0.135 Angle : 0.560 7.394 17864 Z= 0.309 Chirality : 0.040 0.171 1960 Planarity : 0.004 0.070 1969 Dihedral : 17.190 80.951 2562 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.03 % Allowed : 16.08 % 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 aren not related in a simple way. whole: -3.35 (0.22), residues: 1296 helix: -1.78 (0.22), residues: 513 sheet: -1.85 (0.53), residues: 88 loop : -2.67 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.026 0.001 TYR A 112 PHE 0.019 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 covalent geometry : bond 0.00303 (12972) covalent geometry : angle 0.55998 (17864) hydrogen bonds : bond 0.04580 ( 271) hydrogen bonds : angle 5.10042 ( 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 173 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7206 (mmtt) REVERT: A 96 LYS cc_start: 0.7930 (tttt) cc_final: 0.7478 (tptp) REVERT: A 394 LYS cc_start: 0.7234 (tttp) cc_final: 0.6803 (ttpt) REVERT: A 485 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6469 (tp) REVERT: A 487 MET cc_start: 0.6801 (mmp) cc_final: 0.6240 (ptt) REVERT: A 626 ASP cc_start: 0.7474 (t70) cc_final: 0.7055 (t70) REVERT: A 640 ILE cc_start: 0.7087 (tp) cc_final: 0.6847 (pt) REVERT: A 660 LYS cc_start: 0.5011 (tmtt) cc_final: 0.3295 (tptm) REVERT: A 729 SER cc_start: 0.7810 (p) cc_final: 0.7205 (t) REVERT: A 962 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7919 (mmmt) REVERT: A 1010 PHE cc_start: 0.6257 (t80) cc_final: 0.5546 (t80) REVERT: A 1065 LYS cc_start: 0.6851 (mttt) cc_final: 0.6112 (mmmt) outliers start: 35 outliers final: 29 residues processed: 161 average time/residue: 0.1154 time to fit residues: 27.3609 Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 260 LEU 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 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE 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 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 940 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 694 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.189641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152028 restraints weight = 14256.688| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.04 r_work: 0.3612 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12972 Z= 0.129 Angle : 0.559 6.939 17864 Z= 0.308 Chirality : 0.039 0.169 1960 Planarity : 0.004 0.072 1969 Dihedral : 17.128 80.035 2562 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 2.77 % Allowed : 16.59 % 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 aren not related in a simple way. whole: -3.18 (0.22), residues: 1296 helix: -1.56 (0.23), residues: 505 sheet: -1.83 (0.53), residues: 89 loop : -2.63 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.024 0.001 TYR A 112 PHE 0.020 0.001 PHE A 362 TRP 0.026 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00289 (12972) covalent geometry : angle 0.55891 (17864) hydrogen bonds : bond 0.04438 ( 271) hydrogen bonds : angle 5.03945 ( 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 168 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7446 (mmtt) cc_final: 0.7239 (mmtt) REVERT: A 96 LYS cc_start: 0.8051 (tttt) cc_final: 0.7596 (tptp) REVERT: A 394 LYS cc_start: 0.7188 (tttp) cc_final: 0.6708 (ttpt) REVERT: A 485 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6376 (tp) REVERT: A 487 MET cc_start: 0.6736 (mmp) cc_final: 0.6198 (ptt) REVERT: A 626 ASP cc_start: 0.7503 (t70) cc_final: 0.7062 (t70) REVERT: A 640 ILE cc_start: 0.7053 (tp) cc_final: 0.6843 (pt) REVERT: A 660 LYS cc_start: 0.5042 (tmtt) cc_final: 0.3536 (tttt) REVERT: A 729 SER cc_start: 0.7861 (p) cc_final: 0.7277 (t) REVERT: A 939 ASP cc_start: 0.6843 (m-30) cc_final: 0.6561 (m-30) REVERT: A 962 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7884 (mmmt) REVERT: A 1010 PHE cc_start: 0.6174 (t80) cc_final: 0.5938 (t80) REVERT: A 1065 LYS cc_start: 0.6680 (mttt) cc_final: 0.5816 (mmmt) outliers start: 32 outliers final: 28 residues processed: 156 average time/residue: 0.1052 time to fit residues: 24.9610 Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 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 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 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 940 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 68 optimal weight: 0.0970 chunk 36 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 495 ASN ** A 901 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 = 0.4313 r_free = 0.4313 target = 0.194932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161180 restraints weight = 14104.554| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.85 r_work: 0.3704 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12972 Z= 0.111 Angle : 0.553 10.800 17864 Z= 0.302 Chirality : 0.039 0.187 1960 Planarity : 0.004 0.074 1969 Dihedral : 17.001 79.610 2562 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 2.33 % Allowed : 16.94 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.23), residues: 1296 helix: -1.33 (0.23), residues: 502 sheet: -1.80 (0.52), residues: 91 loop : -2.57 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.022 0.001 TYR A 112 PHE 0.017 0.001 PHE A 362 TRP 0.022 0.001 TRP A 141 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00241 (12972) covalent geometry : angle 0.55272 (17864) hydrogen bonds : bond 0.04221 ( 271) hydrogen bonds : angle 4.87432 ( 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 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7399 (mmtt) cc_final: 0.7190 (mmtt) REVERT: A 96 LYS cc_start: 0.8016 (tttt) cc_final: 0.7600 (tptp) REVERT: A 288 LYS cc_start: 0.8624 (pttt) cc_final: 0.8373 (pttp) REVERT: A 342 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5694 (pp) REVERT: A 394 LYS cc_start: 0.7051 (tttp) cc_final: 0.6608 (ttmt) REVERT: A 485 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6217 (tp) REVERT: A 487 MET cc_start: 0.6652 (mmp) cc_final: 0.6336 (ptt) REVERT: A 626 ASP cc_start: 0.7383 (t70) cc_final: 0.6990 (t70) REVERT: A 640 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6770 (pt) REVERT: A 660 LYS cc_start: 0.5076 (tmtt) cc_final: 0.3344 (tptm) REVERT: A 729 SER cc_start: 0.7720 (p) cc_final: 0.7160 (t) REVERT: A 939 ASP cc_start: 0.6552 (m-30) cc_final: 0.6317 (m-30) REVERT: A 962 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7928 (mmmt) REVERT: A 1010 PHE cc_start: 0.6164 (t80) cc_final: 0.5914 (t80) REVERT: A 1065 LYS cc_start: 0.6510 (mttt) cc_final: 0.5794 (mmmt) outliers start: 27 outliers final: 19 residues processed: 154 average time/residue: 0.1078 time to fit residues: 24.9628 Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 404 GLN 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 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1003 VAL 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: 0.8980 chunk 129 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 404 GLN A1118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.184734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146451 restraints weight = 14457.528| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.30 r_work: 0.3543 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12972 Z= 0.211 Angle : 0.637 10.746 17864 Z= 0.346 Chirality : 0.043 0.191 1960 Planarity : 0.004 0.072 1969 Dihedral : 17.269 80.992 2562 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 2.33 % Allowed : 17.11 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.22), residues: 1296 helix: -1.43 (0.23), residues: 510 sheet: -1.85 (0.53), residues: 89 loop : -2.59 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 692 TYR 0.023 0.002 TYR A 112 PHE 0.021 0.002 PHE A 888 TRP 0.024 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00486 (12972) covalent geometry : angle 0.63684 (17864) hydrogen bonds : bond 0.05231 ( 271) hydrogen bonds : angle 5.19142 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.97 seconds wall clock time: 49 minutes 41.78 seconds (2981.78 seconds total)