Starting phenix.real_space_refine on Sun Aug 24 03:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2b_50146/08_2025/9f2b_50146.map" } resolution = 3.49 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6643 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 7197 2.51 5 N 1828 2.21 5 O 2143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 906 Classifications: {'peptide': 106} Link IDs: {'TRANS': 105} Chain: "B" Number of atoms: 10204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10204 Classifications: {'peptide': 1253} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1214} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.34, per 1000 atoms: 0.21 Number of scatterers: 11208 At special positions: 0 Unit cell: (89.05, 115.7, 169.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2143 8.00 N 1828 7.00 C 7197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 454 " distance=2.04 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 Links applied ALPHA1-6 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 5 " NAG-ASN " NAG A 701 " - " ASN A 441 " " NAG C 1 " - " ASN A 491 " " NAG D 1 " - " ASN A 516 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 502.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 17 sheets defined 31.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.545A pdb=" N MET A 427 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.832A pdb=" N THR B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.639A pdb=" N THR B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.606A pdb=" N ILE B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 300 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.512A pdb=" N MET B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 347 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.736A pdb=" N ASN B 470 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 471 " --> pdb=" O GLU B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 471' Processing helix chain 'B' and resid 496 through 506 Processing helix chain 'B' and resid 549 through 557 removed outlier: 3.508A pdb=" N GLN B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 602 through 619 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 643 through 646 removed outlier: 3.906A pdb=" N MET B 646 " --> pdb=" O ILE B 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 643 through 646' Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'B' and resid 689 through 721 Processing helix chain 'B' and resid 721 through 753 removed outlier: 3.633A pdb=" N GLN B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 765 through 800 removed outlier: 4.274A pdb=" N LEU B 769 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 783 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 824 removed outlier: 3.863A pdb=" N GLY B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 807 " --> pdb=" O TYR B 803 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 4.076A pdb=" N THR B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.559A pdb=" N LYS B 855 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 872 removed outlier: 3.646A pdb=" N THR B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1266 through 1270 removed outlier: 3.799A pdb=" N GLN B1270 " --> pdb=" O TYR B1267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.407A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.407A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR A 488 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A 467 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LYS A 490 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 469 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 489 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 439 through 440 removed outlier: 6.280A pdb=" N PHE A 459 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 499 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 removed outlier: 3.733A pdb=" N VAL B 137 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 136 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 21 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS B 34 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 155 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 47 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 152 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 164 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA7, first strand: chain 'B' and resid 213 through 214 removed outlier: 4.491A pdb=" N VAL B 373 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 458 removed outlier: 7.943A pdb=" N TYR B 426 " --> pdb=" O LYS B 541 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N TYR B 543 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 428 " --> pdb=" O TYR B 543 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU B 545 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS B 430 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 479 through 481 Processing sheet with id=AB1, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.335A pdb=" N ALA B 567 " --> pdb=" O VAL B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AB3, first strand: chain 'B' and resid 895 through 900 removed outlier: 4.192A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 904 through 906 removed outlier: 4.304A pdb=" N PHE B1072 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 944 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B1074 " --> pdb=" O SER B 942 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER B 942 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AB6, first strand: chain 'B' and resid 1122 through 1126 Processing sheet with id=AB7, first strand: chain 'B' and resid 1160 through 1164 removed outlier: 5.602A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1160 through 1164 removed outlier: 3.513A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2669 1.33 - 1.45: 2521 1.45 - 1.58: 6193 1.58 - 1.70: 1 1.70 - 1.82: 67 Bond restraints: 11451 Sorted by residual: bond pdb=" N ILE B 634 " pdb=" CA ILE B 634 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.30e-03 1.88e+04 1.56e+01 bond pdb=" N VAL B 621 " pdb=" CA VAL B 621 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.24e-02 6.50e+03 8.67e+00 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.589 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" N THR B 624 " pdb=" CA THR B 624 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.28e-02 6.10e+03 6.93e+00 bond pdb=" N SER B 622 " pdb=" CA SER B 622 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.79e+00 ... (remaining 11446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15119 1.92 - 3.83: 323 3.83 - 5.75: 40 5.75 - 7.66: 8 7.66 - 9.58: 2 Bond angle restraints: 15492 Sorted by residual: angle pdb=" CA ILE B 632 " pdb=" C ILE B 632 " pdb=" O ILE B 632 " ideal model delta sigma weight residual 121.70 117.68 4.02 1.06e+00 8.90e-01 1.44e+01 angle pdb=" CA VAL B1180 " pdb=" C VAL B1180 " pdb=" O VAL B1180 " ideal model delta sigma weight residual 121.63 117.88 3.75 9.90e-01 1.02e+00 1.44e+01 angle pdb=" CA ASP B1178 " pdb=" C ASP B1178 " pdb=" O ASP B1178 " ideal model delta sigma weight residual 121.87 117.57 4.30 1.16e+00 7.43e-01 1.37e+01 angle pdb=" N LYS B 626 " pdb=" CA LYS B 626 " pdb=" C LYS B 626 " ideal model delta sigma weight residual 112.87 108.45 4.42 1.20e+00 6.94e-01 1.36e+01 angle pdb=" CA PHE B 194 " pdb=" CB PHE B 194 " pdb=" CG PHE B 194 " ideal model delta sigma weight residual 113.80 117.34 -3.54 1.00e+00 1.00e+00 1.25e+01 ... (remaining 15487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.03: 6239 24.03 - 48.05: 579 48.05 - 72.08: 78 72.08 - 96.11: 12 96.11 - 120.13: 24 Dihedral angle restraints: 6932 sinusoidal: 2911 harmonic: 4021 Sorted by residual: dihedral pdb=" C2 FUC D 5 " pdb=" C1 FUC D 5 " pdb=" O5 FUC D 5 " pdb=" C5 FUC D 5 " ideal model delta sinusoidal sigma weight residual 57.68 -62.45 120.13 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA GLN B 7 " pdb=" C GLN B 7 " pdb=" N PHE B 8 " pdb=" CA PHE B 8 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" C2 MAN D 4 " pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " pdb=" C5 MAN D 4 " ideal model delta sinusoidal sigma weight residual -57.62 54.83 -112.45 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.964: 1719 0.964 - 1.928: 0 1.928 - 2.892: 0 2.892 - 3.856: 1 3.856 - 4.820: 1 Chirality restraints: 1721 Sorted by residual: chirality pdb=" C1 FUC C 2 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 2 " pdb=" O5 FUC C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.42 -4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 0.69 -3.09 2.00e-02 2.50e+03 2.39e+04 chirality pdb=" C1 MAN D 4 " pdb=" O6 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.86e+01 ... (remaining 1718 not shown) Planarity restraints: 1979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.184 2.00e-02 2.50e+03 1.52e-01 2.89e+02 pdb=" C7 NAG C 1 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.247 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 516 " -0.067 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" CG ASN A 516 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 516 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 516 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 491 " 0.061 2.00e-02 2.50e+03 6.33e-02 5.01e+01 pdb=" CG ASN A 491 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 491 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 491 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.067 2.00e-02 2.50e+03 ... (remaining 1976 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 468 2.72 - 3.26: 11298 3.26 - 3.81: 17715 3.81 - 4.35: 21782 4.35 - 4.90: 37792 Nonbonded interactions: 89055 Sorted by model distance: nonbonded pdb=" OD1 ASP B 461 " pdb=" NZ LYS B 731 " model vdw 2.172 3.120 nonbonded pdb=" O LYS B 840 " pdb=" OG1 THR B 844 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 755 " pdb=" OE1 GLU B 758 " model vdw 2.219 3.040 nonbonded pdb=" O LYS B 903 " pdb=" OG SER B 922 " model vdw 2.253 3.040 nonbonded pdb=" O GLN B1003 " pdb=" ND2 ASN B1151 " model vdw 2.269 3.120 ... (remaining 89050 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: 14.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.007 0.428 11460 Z= 0.364 Angle : 0.730 16.322 15518 Z= 0.387 Chirality : 0.147 4.820 1721 Planarity : 0.006 0.177 1976 Dihedral : 18.899 120.135 4339 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.97 % Allowed : 24.70 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.16 (0.23), residues: 1345 helix: 2.60 (0.27), residues: 369 sheet: -0.33 (0.34), residues: 218 loop : -1.08 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 893 TYR 0.019 0.001 TYR B 751 PHE 0.021 0.001 PHE B 194 TRP 0.015 0.001 TRP B1266 HIS 0.004 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00442 (11451) covalent geometry : angle 0.65029 (15492) SS BOND : bond 0.00519 ( 1) SS BOND : angle 1.43809 ( 2) hydrogen bonds : bond 0.12298 ( 425) hydrogen bonds : angle 5.27610 ( 1197) link_ALPHA1-6 : bond 0.03860 ( 1) link_ALPHA1-6 : angle 3.78169 ( 3) link_BETA1-4 : bond 0.02745 ( 2) link_BETA1-4 : angle 9.60575 ( 6) link_BETA1-6 : bond 0.02682 ( 2) link_BETA1-6 : angle 3.15546 ( 6) link_NAG-ASN : bond 0.34999 ( 3) link_NAG-ASN : angle 10.80364 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.7572 (pt) cc_final: 0.7309 (mt) REVERT: A 478 TYR cc_start: 0.7678 (t80) cc_final: 0.7163 (t80) REVERT: A 483 THR cc_start: 0.8170 (m) cc_final: 0.7970 (m) REVERT: B 884 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: B 1054 MET cc_start: 0.7629 (mmp) cc_final: 0.7297 (mmt) outliers start: 12 outliers final: 2 residues processed: 163 average time/residue: 0.1094 time to fit residues: 25.6137 Evaluate side-chains 136 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 884 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 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 447 GLN B 31 GLN B 39 HIS B 224 GLN B 288 ASN B 404 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 533 ASN B 570 ASN B 697 ASN B 739 GLN B 765 ASN B 778 ASN B 913 GLN B 954 ASN B1026 ASN B1147 ASN B1199 GLN B1216 ASN B1233 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102536 restraints weight = 19279.303| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.60 r_work: 0.3158 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11460 Z= 0.157 Angle : 0.584 13.069 15518 Z= 0.299 Chirality : 0.047 0.474 1721 Planarity : 0.003 0.052 1976 Dihedral : 12.555 121.388 1638 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.18 % Allowed : 24.13 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.28 (0.23), residues: 1345 helix: 2.66 (0.27), residues: 369 sheet: -0.30 (0.34), residues: 225 loop : -0.98 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.015 0.001 TYR A 488 PHE 0.018 0.001 PHE A 464 TRP 0.008 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00363 (11451) covalent geometry : angle 0.56418 (15492) SS BOND : bond 0.00321 ( 1) SS BOND : angle 1.23390 ( 2) hydrogen bonds : bond 0.04437 ( 425) hydrogen bonds : angle 4.50508 ( 1197) link_ALPHA1-6 : bond 0.00494 ( 1) link_ALPHA1-6 : angle 3.27637 ( 3) link_BETA1-4 : bond 0.01226 ( 2) link_BETA1-4 : angle 1.89171 ( 6) link_BETA1-6 : bond 0.01692 ( 2) link_BETA1-6 : angle 3.38990 ( 6) link_NAG-ASN : bond 0.00684 ( 3) link_NAG-ASN : angle 5.21284 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8145 (pt) cc_final: 0.7759 (mt) REVERT: B 198 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: B 461 ASP cc_start: 0.8645 (t0) cc_final: 0.8425 (t0) REVERT: B 758 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: B 884 GLU cc_start: 0.8238 (tt0) cc_final: 0.7928 (mt-10) outliers start: 27 outliers final: 14 residues processed: 156 average time/residue: 0.1078 time to fit residues: 24.8973 Evaluate side-chains 145 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 561 HIS Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1025 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN B 875 ASN B1064 HIS B1199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099903 restraints weight = 19852.466| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.75 r_work: 0.3100 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11460 Z= 0.246 Angle : 0.634 13.325 15518 Z= 0.329 Chirality : 0.048 0.451 1721 Planarity : 0.004 0.047 1976 Dihedral : 10.702 119.912 1635 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.60 % Allowed : 23.73 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.01 (0.23), residues: 1345 helix: 2.44 (0.27), residues: 369 sheet: -0.68 (0.32), residues: 240 loop : -1.09 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 555 TYR 0.017 0.002 TYR A 488 PHE 0.024 0.002 PHE A 489 TRP 0.009 0.001 TRP B 717 HIS 0.006 0.001 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00595 (11451) covalent geometry : angle 0.61850 (15492) SS BOND : bond 0.00219 ( 1) SS BOND : angle 1.72373 ( 2) hydrogen bonds : bond 0.04904 ( 425) hydrogen bonds : angle 4.57160 ( 1197) link_ALPHA1-6 : bond 0.01075 ( 1) link_ALPHA1-6 : angle 2.03946 ( 3) link_BETA1-4 : bond 0.00811 ( 2) link_BETA1-4 : angle 1.82485 ( 6) link_BETA1-6 : bond 0.01077 ( 2) link_BETA1-6 : angle 2.55463 ( 6) link_NAG-ASN : bond 0.00882 ( 3) link_NAG-ASN : angle 5.19168 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8147 (pt) cc_final: 0.7818 (mt) REVERT: A 501 ASN cc_start: 0.8638 (t0) cc_final: 0.8274 (t0) REVERT: B 56 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: B 67 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7321 (mp10) REVERT: B 461 ASP cc_start: 0.8904 (t0) cc_final: 0.8588 (t0) REVERT: B 646 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7112 (pmm) REVERT: B 758 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: B 884 GLU cc_start: 0.8266 (tt0) cc_final: 0.8052 (mt-10) REVERT: B 934 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8598 (p90) outliers start: 57 outliers final: 33 residues processed: 163 average time/residue: 0.1039 time to fit residues: 25.1879 Evaluate side-chains 154 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099123 restraints weight = 19636.764| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.72 r_work: 0.3093 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11460 Z= 0.133 Angle : 0.543 11.982 15518 Z= 0.280 Chirality : 0.045 0.457 1721 Planarity : 0.003 0.043 1976 Dihedral : 9.816 112.922 1628 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.31 % Allowed : 24.94 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.20 (0.23), residues: 1345 helix: 2.67 (0.27), residues: 368 sheet: -0.58 (0.32), residues: 239 loop : -0.98 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 513 TYR 0.013 0.001 TYR B1030 PHE 0.017 0.001 PHE A 473 TRP 0.022 0.001 TRP B1266 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00310 (11451) covalent geometry : angle 0.52625 (15492) SS BOND : bond 0.00369 ( 1) SS BOND : angle 1.35950 ( 2) hydrogen bonds : bond 0.04075 ( 425) hydrogen bonds : angle 4.36098 ( 1197) link_ALPHA1-6 : bond 0.01300 ( 1) link_ALPHA1-6 : angle 2.22956 ( 3) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 1.65576 ( 6) link_BETA1-6 : bond 0.01242 ( 2) link_BETA1-6 : angle 2.62472 ( 6) link_NAG-ASN : bond 0.00744 ( 3) link_NAG-ASN : angle 4.80399 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8175 (pt) cc_final: 0.7835 (mt) REVERT: A 501 ASN cc_start: 0.8627 (t0) cc_final: 0.8085 (t0) REVERT: B 56 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: B 461 ASP cc_start: 0.8894 (t0) cc_final: 0.8537 (t0) REVERT: B 646 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7096 (pmm) REVERT: B 758 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 759 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7791 (mtmm) REVERT: B 884 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7979 (mt-10) outliers start: 41 outliers final: 27 residues processed: 153 average time/residue: 0.1076 time to fit residues: 24.3716 Evaluate side-chains 150 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 561 HIS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 17 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 150 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN B 860 GLN B1245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098869 restraints weight = 19879.315| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.73 r_work: 0.3084 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11460 Z= 0.269 Angle : 0.632 12.911 15518 Z= 0.327 Chirality : 0.048 0.437 1721 Planarity : 0.004 0.045 1976 Dihedral : 10.060 114.726 1628 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.08 % Allowed : 23.73 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.10 (0.23), residues: 1345 helix: 2.35 (0.27), residues: 369 sheet: -0.82 (0.31), residues: 240 loop : -1.10 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 861 TYR 0.014 0.002 TYR B1030 PHE 0.030 0.002 PHE A 473 TRP 0.011 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00651 (11451) covalent geometry : angle 0.61729 (15492) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.81167 ( 2) hydrogen bonds : bond 0.04817 ( 425) hydrogen bonds : angle 4.59091 ( 1197) link_ALPHA1-6 : bond 0.01253 ( 1) link_ALPHA1-6 : angle 2.41325 ( 3) link_BETA1-4 : bond 0.00666 ( 2) link_BETA1-4 : angle 1.39521 ( 6) link_BETA1-6 : bond 0.00963 ( 2) link_BETA1-6 : angle 2.71405 ( 6) link_NAG-ASN : bond 0.00894 ( 3) link_NAG-ASN : angle 4.93754 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5805 (mptt) REVERT: A 448 ILE cc_start: 0.8251 (pt) cc_final: 0.7915 (mt) REVERT: A 501 ASN cc_start: 0.8668 (t0) cc_final: 0.8084 (t0) REVERT: A 522 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7916 (mm-40) REVERT: B 56 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: B 67 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7430 (mp10) REVERT: B 461 ASP cc_start: 0.8986 (t0) cc_final: 0.8626 (t0) REVERT: B 646 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7106 (pmm) REVERT: B 758 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 884 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 63 outliers final: 41 residues processed: 165 average time/residue: 0.1111 time to fit residues: 26.7630 Evaluate side-chains 160 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 889 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 chunk 119 optimal weight: 0.0470 chunk 134 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100074 restraints weight = 19427.259| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.73 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11460 Z= 0.102 Angle : 0.535 11.495 15518 Z= 0.273 Chirality : 0.045 0.450 1721 Planarity : 0.003 0.042 1976 Dihedral : 9.167 105.830 1628 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.74 % Allowed : 25.42 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.27 (0.23), residues: 1345 helix: 2.77 (0.27), residues: 368 sheet: -0.54 (0.32), residues: 233 loop : -0.96 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 861 TYR 0.014 0.001 TYR B1030 PHE 0.021 0.001 PHE A 473 TRP 0.012 0.001 TRP B1266 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00216 (11451) covalent geometry : angle 0.51952 (15492) SS BOND : bond 0.00482 ( 1) SS BOND : angle 1.26488 ( 2) hydrogen bonds : bond 0.03748 ( 425) hydrogen bonds : angle 4.28672 ( 1197) link_ALPHA1-6 : bond 0.01575 ( 1) link_ALPHA1-6 : angle 2.69616 ( 3) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 1.59232 ( 6) link_BETA1-6 : bond 0.01241 ( 2) link_BETA1-6 : angle 2.49833 ( 6) link_NAG-ASN : bond 0.00745 ( 3) link_NAG-ASN : angle 4.51039 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8233 (pt) cc_final: 0.7875 (mt) REVERT: A 501 ASN cc_start: 0.8660 (t0) cc_final: 0.8035 (t0) REVERT: B 67 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7334 (mp10) REVERT: B 461 ASP cc_start: 0.8914 (t0) cc_final: 0.8525 (t0) REVERT: B 646 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7138 (pmm) REVERT: B 758 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 884 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7964 (mt-10) outliers start: 34 outliers final: 20 residues processed: 148 average time/residue: 0.1045 time to fit residues: 22.7896 Evaluate side-chains 143 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 561 HIS Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.094561 restraints weight = 19797.726| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.72 r_work: 0.3035 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 11460 Z= 0.313 Angle : 0.676 12.999 15518 Z= 0.348 Chirality : 0.049 0.437 1721 Planarity : 0.004 0.045 1976 Dihedral : 9.616 112.018 1628 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.28 % Allowed : 24.62 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.17 (0.23), residues: 1345 helix: 2.31 (0.27), residues: 369 sheet: -0.83 (0.32), residues: 235 loop : -1.17 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 861 TYR 0.014 0.002 TYR B1030 PHE 0.029 0.002 PHE A 489 TRP 0.010 0.002 TRP B 717 HIS 0.005 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00764 (11451) covalent geometry : angle 0.66180 (15492) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.98871 ( 2) hydrogen bonds : bond 0.04957 ( 425) hydrogen bonds : angle 4.64576 ( 1197) link_ALPHA1-6 : bond 0.01649 ( 1) link_ALPHA1-6 : angle 2.59727 ( 3) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 1.40799 ( 6) link_BETA1-6 : bond 0.00873 ( 2) link_BETA1-6 : angle 2.76732 ( 6) link_NAG-ASN : bond 0.00726 ( 3) link_NAG-ASN : angle 4.88150 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8308 (pttp) REVERT: A 428 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5889 (mptt) REVERT: A 448 ILE cc_start: 0.8296 (pt) cc_final: 0.7960 (mt) REVERT: A 501 ASN cc_start: 0.8705 (t0) cc_final: 0.8051 (t0) REVERT: A 507 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7948 (p-80) REVERT: B 67 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7474 (mp10) REVERT: B 148 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: B 461 ASP cc_start: 0.9050 (t0) cc_final: 0.8682 (t0) REVERT: B 646 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7070 (pmm) REVERT: B 758 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 879 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 884 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7969 (mt-10) outliers start: 53 outliers final: 31 residues processed: 157 average time/residue: 0.1061 time to fit residues: 24.4165 Evaluate side-chains 153 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095354 restraints weight = 19626.305| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.71 r_work: 0.3039 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11460 Z= 0.232 Angle : 0.620 12.377 15518 Z= 0.319 Chirality : 0.047 0.450 1721 Planarity : 0.004 0.044 1976 Dihedral : 9.101 110.949 1628 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.71 % Allowed : 25.50 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.21 (0.23), residues: 1345 helix: 2.27 (0.27), residues: 375 sheet: -0.89 (0.32), residues: 235 loop : -1.20 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 861 TYR 0.015 0.001 TYR A 478 PHE 0.025 0.002 PHE A 473 TRP 0.009 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00561 (11451) covalent geometry : angle 0.60636 (15492) SS BOND : bond 0.00856 ( 1) SS BOND : angle 1.98790 ( 2) hydrogen bonds : bond 0.04612 ( 425) hydrogen bonds : angle 4.56277 ( 1197) link_ALPHA1-6 : bond 0.02005 ( 1) link_ALPHA1-6 : angle 2.02758 ( 3) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 1.59926 ( 6) link_BETA1-6 : bond 0.00899 ( 2) link_BETA1-6 : angle 2.75659 ( 6) link_NAG-ASN : bond 0.00603 ( 3) link_NAG-ASN : angle 4.66684 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5952 (mmtt) REVERT: A 448 ILE cc_start: 0.8287 (pt) cc_final: 0.7944 (mt) REVERT: A 501 ASN cc_start: 0.8696 (t0) cc_final: 0.8020 (t0) REVERT: B 67 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7471 (mp10) REVERT: B 106 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: B 148 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: B 461 ASP cc_start: 0.9055 (t0) cc_final: 0.8688 (t0) REVERT: B 646 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7117 (pmm) REVERT: B 758 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: B 879 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 884 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 934 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8382 (p90) outliers start: 46 outliers final: 31 residues processed: 152 average time/residue: 0.1015 time to fit residues: 22.3284 Evaluate side-chains 153 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 889 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098362 restraints weight = 19260.206| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.78 r_work: 0.3077 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11460 Z= 0.130 Angle : 0.557 11.593 15518 Z= 0.286 Chirality : 0.045 0.438 1721 Planarity : 0.003 0.043 1976 Dihedral : 8.332 107.115 1628 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.91 % Allowed : 26.47 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.03 (0.23), residues: 1345 helix: 2.57 (0.27), residues: 374 sheet: -0.76 (0.32), residues: 235 loop : -1.11 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 861 TYR 0.014 0.001 TYR B1030 PHE 0.023 0.001 PHE A 473 TRP 0.011 0.001 TRP B1266 HIS 0.010 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00298 (11451) covalent geometry : angle 0.54254 (15492) SS BOND : bond 0.00645 ( 1) SS BOND : angle 1.66221 ( 2) hydrogen bonds : bond 0.03969 ( 425) hydrogen bonds : angle 4.36328 ( 1197) link_ALPHA1-6 : bond 0.02041 ( 1) link_ALPHA1-6 : angle 1.46529 ( 3) link_BETA1-4 : bond 0.00484 ( 2) link_BETA1-4 : angle 1.86974 ( 6) link_BETA1-6 : bond 0.01082 ( 2) link_BETA1-6 : angle 2.59896 ( 6) link_NAG-ASN : bond 0.00582 ( 3) link_NAG-ASN : angle 4.41272 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8314 (pt) cc_final: 0.7978 (mt) REVERT: A 475 ASP cc_start: 0.8488 (m-30) cc_final: 0.8072 (m-30) REVERT: A 476 GLU cc_start: 0.8345 (mp0) cc_final: 0.7537 (tp30) REVERT: B 67 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7443 (mp10) REVERT: B 148 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: B 461 ASP cc_start: 0.8988 (t0) cc_final: 0.8612 (t0) REVERT: B 646 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7118 (pmm) REVERT: B 758 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 884 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 934 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8345 (p90) outliers start: 36 outliers final: 28 residues processed: 151 average time/residue: 0.1029 time to fit residues: 22.8057 Evaluate side-chains 154 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS A 507 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 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 = 0.3495 r_free = 0.3495 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097408 restraints weight = 19632.975| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.75 r_work: 0.3063 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11460 Z= 0.163 Angle : 0.575 11.618 15518 Z= 0.295 Chirality : 0.046 0.430 1721 Planarity : 0.003 0.043 1976 Dihedral : 8.335 106.990 1628 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.07 % Allowed : 25.99 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.01 (0.23), residues: 1345 helix: 2.52 (0.27), residues: 374 sheet: -0.74 (0.32), residues: 235 loop : -1.11 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 861 TYR 0.018 0.001 TYR A 478 PHE 0.024 0.001 PHE A 473 TRP 0.012 0.001 TRP B1266 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00388 (11451) covalent geometry : angle 0.56047 (15492) SS BOND : bond 0.00503 ( 1) SS BOND : angle 1.73322 ( 2) hydrogen bonds : bond 0.04091 ( 425) hydrogen bonds : angle 4.37016 ( 1197) link_ALPHA1-6 : bond 0.01809 ( 1) link_ALPHA1-6 : angle 1.41482 ( 3) link_BETA1-4 : bond 0.00552 ( 2) link_BETA1-4 : angle 1.98131 ( 6) link_BETA1-6 : bond 0.00997 ( 2) link_BETA1-6 : angle 2.62230 ( 6) link_NAG-ASN : bond 0.00691 ( 3) link_NAG-ASN : angle 4.45896 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8330 (pt) cc_final: 0.7998 (mt) REVERT: A 475 ASP cc_start: 0.8491 (m-30) cc_final: 0.8099 (m-30) REVERT: A 476 GLU cc_start: 0.8389 (mp0) cc_final: 0.7603 (tp30) REVERT: B 67 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7466 (mp10) REVERT: B 148 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: B 461 ASP cc_start: 0.9000 (t0) cc_final: 0.8638 (t0) REVERT: B 646 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7157 (pmm) REVERT: B 758 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: B 879 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 884 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: B 934 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8395 (p90) REVERT: B 1054 MET cc_start: 0.8410 (mmt) cc_final: 0.8198 (mmp) outliers start: 38 outliers final: 30 residues processed: 150 average time/residue: 0.1125 time to fit residues: 24.4915 Evaluate side-chains 155 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 884 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1220 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1254 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098247 restraints weight = 19614.431| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.73 r_work: 0.3082 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11460 Z= 0.133 Angle : 0.550 11.237 15518 Z= 0.283 Chirality : 0.045 0.423 1721 Planarity : 0.003 0.043 1976 Dihedral : 7.945 103.780 1628 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.15 % Allowed : 26.07 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.09 (0.23), residues: 1345 helix: 2.61 (0.27), residues: 374 sheet: -0.68 (0.32), residues: 235 loop : -1.07 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 861 TYR 0.022 0.001 TYR A 478 PHE 0.023 0.001 PHE A 473 TRP 0.015 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00312 (11451) covalent geometry : angle 0.53600 (15492) SS BOND : bond 0.00532 ( 1) SS BOND : angle 1.62729 ( 2) hydrogen bonds : bond 0.03846 ( 425) hydrogen bonds : angle 4.25670 ( 1197) link_ALPHA1-6 : bond 0.01671 ( 1) link_ALPHA1-6 : angle 1.28712 ( 3) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 2.07554 ( 6) link_BETA1-6 : bond 0.01145 ( 2) link_BETA1-6 : angle 2.65822 ( 6) link_NAG-ASN : bond 0.00672 ( 3) link_NAG-ASN : angle 4.25725 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2648.06 seconds wall clock time: 46 minutes 35.58 seconds (2795.58 seconds total)