Starting phenix.real_space_refine on Thu Sep 26 08:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_0065.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_0065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_0065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_0065.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/09_2024/6gtg_0065.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, '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: 7.90, per 1000 atoms: 0.63 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.33 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: 5.43 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 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: 1.230 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- 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= 0.535 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 : 6.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (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 TRP 0.024 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 PHE 0.035 0.003 PHE A 258 TYR 0.050 0.004 TYR A 178 ARG 0.014 0.002 ARG A 202 *********************** 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 fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 1.280 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: 0.7407 (tm-30) REVERT: A 394 LYS cc_start: 0.7739 (tttp) cc_final: 0.7516 (ttmt) REVERT: A 535 ASN cc_start: 0.7882 (t160) cc_final: 0.7606 (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: 0.7582 (tptt) REVERT: A 962 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7516 (mmmt) REVERT: A 972 LYS cc_start: 0.8118 (mttm) cc_final: 0.7794 (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: 0.2854 time to fit residues: 113.5290 Evaluate side-chains 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 115 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12972 Z= 0.229 Angle : 0.661 9.384 17864 Z= 0.366 Chirality : 0.042 0.212 1960 Planarity : 0.005 0.067 1969 Dihedral : 18.000 87.067 2563 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 2.94 % Allowed : 11.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.18), residues: 1296 helix: -3.57 (0.16), residues: 508 sheet: -2.49 (0.50), residues: 87 loop : -3.35 (0.20), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 141 HIS 0.007 0.001 HIS A 183 PHE 0.021 0.002 PHE A 681 TYR 0.019 0.002 TYR A 178 ARG 0.004 0.001 ARG A 918 *********************** 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 224 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 SER cc_start: 0.8423 (t) cc_final: 0.8200 (p) REVERT: A 342 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5461 (pp) REVERT: A 353 GLN cc_start: 0.7635 (tm130) cc_final: 0.7283 (tm-30) REVERT: A 458 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.5130 (pp) REVERT: A 640 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7283 (pt) REVERT: A 660 LYS cc_start: 0.5065 (tmtt) cc_final: 0.3346 (tptm) REVERT: A 962 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7757 (mmmt) REVERT: A 972 LYS cc_start: 0.8048 (mttm) cc_final: 0.7831 (mtpt) outliers start: 34 outliers final: 18 residues processed: 214 average time/residue: 0.2512 time to fit residues: 76.9206 Evaluate side-chains 181 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 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 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12972 Z= 0.221 Angle : 0.615 8.513 17864 Z= 0.340 Chirality : 0.041 0.183 1960 Planarity : 0.004 0.065 1969 Dihedral : 17.677 88.250 2562 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 2.85 % Allowed : 13.48 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.19), residues: 1296 helix: -2.96 (0.18), residues: 519 sheet: -2.43 (0.48), residues: 90 loop : -3.22 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 141 HIS 0.007 0.001 HIS A1161 PHE 0.015 0.002 PHE A 888 TYR 0.024 0.002 TYR A1228 ARG 0.003 0.000 ARG A 833 *********************** 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 199 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 SER cc_start: 0.8482 (t) cc_final: 0.8259 (p) REVERT: A 395 ASN cc_start: 0.7363 (t0) cc_final: 0.7154 (t0) REVERT: A 485 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.6677 (tp) REVERT: A 626 ASP cc_start: 0.7170 (t70) cc_final: 0.6764 (t70) REVERT: A 640 ILE cc_start: 0.7482 (tp) cc_final: 0.7198 (pt) REVERT: A 660 LYS cc_start: 0.5087 (tmtt) cc_final: 0.3386 (tptm) REVERT: A 932 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7957 (mmmt) REVERT: A 939 ASP cc_start: 0.6553 (m-30) cc_final: 0.6302 (m-30) REVERT: A 962 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7777 (mmmt) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.2524 time to fit residues: 67.4951 Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 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 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 464 ASN 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 620 ILE 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 123 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 580 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.257 Angle : 0.620 9.945 17864 Z= 0.340 Chirality : 0.042 0.191 1960 Planarity : 0.004 0.065 1969 Dihedral : 17.584 88.046 2562 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 3.89 % Allowed : 13.40 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.20), residues: 1296 helix: -2.67 (0.19), residues: 528 sheet: -2.33 (0.50), residues: 90 loop : -3.08 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.015 0.002 PHE A 888 TYR 0.025 0.002 TYR A 420 ARG 0.003 0.000 ARG A 833 *********************** 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 209 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 485 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6601 (tp) REVERT: A 626 ASP cc_start: 0.7157 (t70) cc_final: 0.6737 (t70) REVERT: A 660 LYS cc_start: 0.4864 (tmtt) cc_final: 0.3399 (tptp) REVERT: A 932 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8024 (mmmt) REVERT: A 939 ASP cc_start: 0.6653 (m-30) cc_final: 0.6385 (m-30) REVERT: A 962 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7818 (mmmt) REVERT: A 1056 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5477 (mt0) outliers start: 45 outliers final: 31 residues processed: 193 average time/residue: 0.2334 time to fit residues: 65.5255 Evaluate side-chains 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 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 270 ASN 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 346 SER Chi-restraints excluded: chain A residue 376 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 705 LYS Chi-restraints excluded: chain A residue 886 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 951 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 694 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3530 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= 0.183 Angle : 0.565 7.374 17864 Z= 0.313 Chirality : 0.039 0.174 1960 Planarity : 0.004 0.065 1969 Dihedral : 17.274 82.257 2562 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.11 % Allowed : 14.61 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.21), residues: 1296 helix: -2.30 (0.21), residues: 521 sheet: -2.11 (0.52), residues: 88 loop : -2.95 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.024 0.001 PHE A1010 TYR 0.026 0.002 TYR A 112 ARG 0.002 0.000 ARG A 833 *********************** 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 fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: A 214 ASN cc_start: 0.7813 (t160) cc_final: 0.7599 (m-40) REVERT: A 485 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6484 (tp) REVERT: A 514 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 626 ASP cc_start: 0.7174 (t70) cc_final: 0.6771 (t70) REVERT: A 660 LYS cc_start: 0.4891 (tmtt) cc_final: 0.3135 (tptm) REVERT: A 932 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8063 (mmmt) REVERT: A 939 ASP cc_start: 0.6574 (m-30) cc_final: 0.6290 (m-30) REVERT: A 962 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7829 (mmmt) outliers start: 36 outliers final: 21 residues processed: 174 average time/residue: 0.2577 time to fit residues: 64.8434 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 86 LEU 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 290 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 599 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12972 Z= 0.340 Angle : 0.651 9.224 17864 Z= 0.355 Chirality : 0.044 0.259 1960 Planarity : 0.004 0.066 1969 Dihedral : 17.567 86.005 2562 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 4.49 % Allowed : 14.26 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.21), residues: 1296 helix: -2.33 (0.21), residues: 522 sheet: -2.07 (0.53), residues: 88 loop : -2.90 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.018 0.002 PHE A 596 TYR 0.023 0.002 TYR A1228 ARG 0.004 0.000 ARG A 833 *********************** 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 196 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 144 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 96 LYS cc_start: 0.7808 (tttt) cc_final: 0.7480 (tptp) REVERT: A 241 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 342 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5279 (pp) REVERT: A 485 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6599 (tp) REVERT: A 626 ASP cc_start: 0.7227 (t70) cc_final: 0.6815 (t70) REVERT: A 660 LYS cc_start: 0.4828 (tmtt) cc_final: 0.3415 (tttt) REVERT: A 932 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8132 (mmmt) REVERT: A 939 ASP cc_start: 0.6719 (m-30) cc_final: 0.6472 (m-30) REVERT: A 962 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7900 (mmmt) outliers start: 52 outliers final: 37 residues processed: 174 average time/residue: 0.2688 time to fit residues: 69.3559 Evaluate side-chains 173 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 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 270 ASN 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 346 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 886 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 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 1168 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 790 ASN A 901 ASN A1070 GLN A1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3847 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= 0.185 Angle : 0.568 7.963 17864 Z= 0.313 Chirality : 0.040 0.189 1960 Planarity : 0.004 0.056 1969 Dihedral : 17.252 81.444 2562 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.72 % Allowed : 15.82 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.21), residues: 1296 helix: -2.18 (0.21), residues: 527 sheet: -2.05 (0.53), residues: 88 loop : -2.81 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.015 0.001 PHE A 362 TYR 0.026 0.001 TYR A 112 ARG 0.007 0.000 ARG A1166 *********************** 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 187 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 144 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: A 15 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6697 (mttm) REVERT: A 96 LYS cc_start: 0.7865 (tttt) cc_final: 0.7502 (tptp) REVERT: A 214 ASN cc_start: 0.7739 (t160) cc_final: 0.7505 (m-40) REVERT: A 456 ILE cc_start: 0.7663 (mm) cc_final: 0.7441 (mm) REVERT: A 485 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6410 (tp) REVERT: A 514 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8207 (mt) REVERT: A 626 ASP cc_start: 0.7172 (t70) cc_final: 0.6776 (t70) REVERT: A 660 LYS cc_start: 0.4756 (tmtt) cc_final: 0.3131 (tptm) REVERT: A 939 ASP cc_start: 0.6612 (m-30) cc_final: 0.6350 (m-30) REVERT: A 962 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7941 (mmmt) outliers start: 43 outliers final: 32 residues processed: 170 average time/residue: 0.2307 time to fit residues: 58.0483 Evaluate side-chains 165 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 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 458 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 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 1168 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 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4092 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= 0.179 Angle : 0.560 9.601 17864 Z= 0.308 Chirality : 0.039 0.202 1960 Planarity : 0.004 0.070 1969 Dihedral : 17.161 80.032 2562 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.20 % Allowed : 16.68 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.22), residues: 1296 helix: -1.85 (0.22), residues: 519 sheet: -1.96 (0.53), residues: 89 loop : -2.75 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.015 0.001 PHE A 362 TYR 0.022 0.001 TYR A 112 ARG 0.007 0.000 ARG A1166 *********************** 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 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 96 LYS cc_start: 0.7883 (tttt) cc_final: 0.7526 (tptp) REVERT: A 214 ASN cc_start: 0.7750 (t160) cc_final: 0.7535 (m-40) REVERT: A 485 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6315 (tp) REVERT: A 514 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (mt) REVERT: A 626 ASP cc_start: 0.7166 (t70) cc_final: 0.6775 (t70) REVERT: A 660 LYS cc_start: 0.4750 (tmtt) cc_final: 0.3008 (tptm) REVERT: A 729 SER cc_start: 0.7674 (p) cc_final: 0.6953 (t) REVERT: A 886 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7816 (pt) REVERT: A 939 ASP cc_start: 0.6602 (m-30) cc_final: 0.6332 (m-30) REVERT: A 962 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7900 (mmmt) REVERT: A 1070 GLN cc_start: 0.6754 (tt0) cc_final: 0.6431 (tt0) outliers start: 37 outliers final: 28 residues processed: 164 average time/residue: 0.2300 time to fit residues: 55.9381 Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 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 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 464 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 940 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 115 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12972 Z= 0.383 Angle : 0.686 10.380 17864 Z= 0.372 Chirality : 0.045 0.212 1960 Planarity : 0.004 0.072 1969 Dihedral : 17.596 85.532 2562 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 3.72 % Allowed : 16.51 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 1296 helix: -2.02 (0.21), residues: 526 sheet: -2.01 (0.54), residues: 88 loop : -2.77 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.019 0.002 PHE A 596 TYR 0.024 0.003 TYR A1228 ARG 0.009 0.001 ARG A1166 *********************** 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 186 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 96 LYS cc_start: 0.7911 (tttt) cc_final: 0.7675 (tptp) REVERT: A 342 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5074 (pp) REVERT: A 397 LYS cc_start: 0.6555 (tppp) cc_final: 0.6064 (tppt) REVERT: A 454 GLU cc_start: 0.6872 (tp30) cc_final: 0.6381 (tp30) REVERT: A 485 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 626 ASP cc_start: 0.7172 (t70) cc_final: 0.6772 (t70) REVERT: A 660 LYS cc_start: 0.4835 (tmtt) cc_final: 0.3556 (tttm) REVERT: A 692 ARG cc_start: 0.7511 (tmt170) cc_final: 0.7277 (ttt90) REVERT: A 939 ASP cc_start: 0.6770 (m-30) cc_final: 0.6515 (m-30) REVERT: A 962 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7859 (mmmt) REVERT: A 1111 LYS cc_start: 0.8357 (mttp) cc_final: 0.8135 (mttp) outliers start: 43 outliers final: 35 residues processed: 169 average time/residue: 0.2386 time to fit residues: 59.9383 Evaluate side-chains 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 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 346 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 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 1086 CYS Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1233 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 130 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 A 607 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12972 Z= 0.212 Angle : 0.596 9.065 17864 Z= 0.329 Chirality : 0.040 0.197 1960 Planarity : 0.004 0.071 1969 Dihedral : 17.294 80.960 2562 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.28 % Allowed : 17.37 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.22), residues: 1296 helix: -1.85 (0.22), residues: 521 sheet: -1.92 (0.54), residues: 89 loop : -2.72 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 141 HIS 0.004 0.001 HIS A 881 PHE 0.016 0.001 PHE A 362 TYR 0.028 0.002 TYR A 112 ARG 0.008 0.000 ARG A1166 ********************** 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 178 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: A 485 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6422 (tp) REVERT: A 514 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 626 ASP cc_start: 0.7155 (t70) cc_final: 0.6759 (t70) REVERT: A 660 LYS cc_start: 0.4715 (tmtt) cc_final: 0.3634 (tttp) REVERT: A 939 ASP cc_start: 0.6705 (m-30) cc_final: 0.6435 (m-30) REVERT: A 955 ASP cc_start: 0.7145 (m-30) cc_final: 0.6723 (m-30) REVERT: A 962 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7937 (mmmt) REVERT: A 1070 GLN cc_start: 0.7016 (tt0) cc_final: 0.6779 (tt0) outliers start: 38 outliers final: 33 residues processed: 166 average time/residue: 0.2442 time to fit residues: 59.9304 Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 346 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 710 PHE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1086 CYS 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 115 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A 942 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.190622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154230 restraints weight = 14072.602| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.96 r_work: 0.3634 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.170 Angle : 0.573 8.017 17864 Z= 0.317 Chirality : 0.039 0.168 1960 Planarity : 0.004 0.074 1969 Dihedral : 17.109 78.466 2562 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.77 % Allowed : 17.72 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.22), residues: 1296 helix: -1.56 (0.22), residues: 513 sheet: -1.74 (0.54), residues: 87 loop : -2.67 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.018 0.001 PHE A 393 TYR 0.026 0.001 TYR A 112 ARG 0.008 0.000 ARG A1166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.11 seconds wall clock time: 48 minutes 35.00 seconds (2915.00 seconds total)