Starting phenix.real_space_refine on Sat Jun 14 23:08:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2b_50146/06_2025/9f2b_50146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2b_50146/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2b_50146/06_2025/9f2b_50146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2b_50146/06_2025/9f2b_50146.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2b_50146/06_2025/9f2b_50146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2b_50146/06_2025/9f2b_50146.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.57, per 1000 atoms: 1.03 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.34 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: 4.53 Time building geometry restraints manager: 3.24 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: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 49.880 ------------------------------------------------------------------------------- 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 : 9.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP B1266 HIS 0.004 0.001 HIS B 223 PHE 0.021 0.001 PHE B 194 TYR 0.019 0.001 TYR B 751 ARG 0.003 0.000 ARG B 893 Details of bonding type rmsd link_NAG-ASN : bond 0.34999 ( 3) link_NAG-ASN : angle 10.80364 ( 9) 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) hydrogen bonds : bond 0.12298 ( 425) hydrogen bonds : angle 5.27610 ( 1197) link_BETA1-6 : bond 0.02682 ( 2) link_BETA1-6 : angle 3.15546 ( 6) SS BOND : bond 0.00519 ( 1) SS BOND : angle 1.43809 ( 2) covalent geometry : bond 0.00442 (11451) covalent geometry : angle 0.65029 (15492) *********************** 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 : 1.169 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: 0.2295 time to fit residues: 54.2597 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 : 1.215 ------------------------------------------------------------------------------- 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 113 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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 B1064 HIS B1147 ASN B1199 GLN B1216 ASN B1233 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100229 restraints weight = 19329.035| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.63 r_work: 0.3114 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11460 Z= 0.235 Angle : 0.640 13.038 15518 Z= 0.329 Chirality : 0.048 0.451 1721 Planarity : 0.004 0.053 1976 Dihedral : 12.606 123.820 1638 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.99 % Allowed : 23.89 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1345 helix: 2.45 (0.27), residues: 370 sheet: -0.50 (0.33), residues: 223 loop : -1.10 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 606 HIS 0.006 0.001 HIS B 552 PHE 0.023 0.002 PHE A 464 TYR 0.017 0.002 TYR A 488 ARG 0.004 0.001 ARG B 187 Details of bonding type rmsd link_NAG-ASN : bond 0.01062 ( 3) link_NAG-ASN : angle 5.37541 ( 9) link_ALPHA1-6 : bond 0.00480 ( 1) link_ALPHA1-6 : angle 2.79063 ( 3) link_BETA1-4 : bond 0.01118 ( 2) link_BETA1-4 : angle 2.39201 ( 6) hydrogen bonds : bond 0.04888 ( 425) hydrogen bonds : angle 4.60901 ( 1197) link_BETA1-6 : bond 0.01217 ( 2) link_BETA1-6 : angle 3.01509 ( 6) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.53515 ( 2) covalent geometry : bond 0.00565 (11451) covalent geometry : angle 0.62140 (15492) *********************** 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 173 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 LEU cc_start: 0.9061 (mt) cc_final: 0.8796 (mp) REVERT: B 56 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: B 67 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7274 (mp10) REVERT: B 461 ASP cc_start: 0.8773 (t0) cc_final: 0.8539 (t0) REVERT: B 758 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: B 884 GLU cc_start: 0.8271 (tt0) cc_final: 0.7941 (mt-10) outliers start: 37 outliers final: 24 residues processed: 162 average time/residue: 0.2112 time to fit residues: 51.2205 Evaluate side-chains 151 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR 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 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 307 THR Chi-restraints excluded: chain B residue 326 ASP 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 626 LYS Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 833 GLN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1220 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.5980 chunk 119 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 899 ASN B1199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100225 restraints weight = 19413.148| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.74 r_work: 0.3110 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11460 Z= 0.130 Angle : 0.539 12.757 15518 Z= 0.277 Chirality : 0.046 0.461 1721 Planarity : 0.003 0.045 1976 Dihedral : 10.189 116.901 1632 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.23 % Allowed : 24.29 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1345 helix: 2.62 (0.27), residues: 374 sheet: -0.53 (0.32), residues: 236 loop : -0.96 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.014 0.001 PHE B 338 TYR 0.013 0.001 TYR B1030 ARG 0.003 0.000 ARG A 513 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 3) link_NAG-ASN : angle 5.02473 ( 9) link_ALPHA1-6 : bond 0.00745 ( 1) link_ALPHA1-6 : angle 2.20957 ( 3) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 1.67930 ( 6) hydrogen bonds : bond 0.04104 ( 425) hydrogen bonds : angle 4.35945 ( 1197) link_BETA1-6 : bond 0.01443 ( 2) link_BETA1-6 : angle 3.08554 ( 6) SS BOND : bond 0.00383 ( 1) SS BOND : angle 1.29510 ( 2) covalent geometry : bond 0.00300 (11451) covalent geometry : angle 0.51980 (15492) *********************** 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 177 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: A 445 GLU cc_start: 0.7119 (pm20) cc_final: 0.6826 (pm20) REVERT: A 501 ASN cc_start: 0.8657 (t0) cc_final: 0.8358 (t0) REVERT: B 67 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7209 (mp10) REVERT: B 461 ASP cc_start: 0.8813 (t0) cc_final: 0.8499 (t0) REVERT: B 561 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: B 758 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: B 884 GLU cc_start: 0.8258 (tt0) cc_final: 0.7950 (mt-10) outliers start: 40 outliers final: 20 residues processed: 162 average time/residue: 0.2191 time to fit residues: 52.2421 Evaluate side-chains 147 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN 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 304 VAL 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 598 THR Chi-restraints excluded: chain B residue 626 LYS 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 849 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 889 ILE Chi-restraints excluded: chain B residue 1025 ASN 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 132 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098084 restraints weight = 19526.372| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.71 r_work: 0.3078 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11460 Z= 0.189 Angle : 0.579 12.142 15518 Z= 0.297 Chirality : 0.046 0.437 1721 Planarity : 0.003 0.043 1976 Dihedral : 9.959 115.680 1632 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.04 % Allowed : 23.97 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1345 helix: 2.63 (0.27), residues: 369 sheet: -0.61 (0.32), residues: 234 loop : -1.01 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.019 0.002 PHE A 489 TYR 0.013 0.001 TYR B1030 ARG 0.003 0.000 ARG A 513 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 3) link_NAG-ASN : angle 4.79020 ( 9) link_ALPHA1-6 : bond 0.01322 ( 1) link_ALPHA1-6 : angle 2.27834 ( 3) link_BETA1-4 : bond 0.00636 ( 2) link_BETA1-4 : angle 1.59727 ( 6) hydrogen bonds : bond 0.04322 ( 425) hydrogen bonds : angle 4.40624 ( 1197) link_BETA1-6 : bond 0.01168 ( 2) link_BETA1-6 : angle 2.52489 ( 6) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.49963 ( 2) covalent geometry : bond 0.00458 (11451) covalent geometry : angle 0.56316 (15492) *********************** 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 173 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: A 462 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7091 (ptm) REVERT: A 501 ASN cc_start: 0.8618 (t0) cc_final: 0.8154 (t0) REVERT: B 56 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: B 67 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7338 (mp10) REVERT: B 461 ASP cc_start: 0.8888 (t0) cc_final: 0.8535 (t0) REVERT: B 498 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8148 (mt) REVERT: B 561 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7117 (t-90) REVERT: B 646 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6810 (pmm) REVERT: B 758 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 759 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7812 (mtmm) REVERT: B 884 GLU cc_start: 0.8296 (tt0) cc_final: 0.8088 (mt-10) REVERT: B 934 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8534 (p90) outliers start: 50 outliers final: 32 residues processed: 158 average time/residue: 0.2202 time to fit residues: 51.4808 Evaluate side-chains 159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 462 MET 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 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 430 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 561 HIS 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 862 LEU Chi-restraints excluded: chain B residue 878 ILE 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 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 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099289 restraints weight = 19446.019| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.72 r_work: 0.3101 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1647 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= 0.127 Angle : 0.534 11.745 15518 Z= 0.274 Chirality : 0.045 0.432 1721 Planarity : 0.003 0.041 1976 Dihedral : 9.348 109.920 1628 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.07 % Allowed : 24.86 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1345 helix: 2.79 (0.27), residues: 368 sheet: -0.53 (0.32), residues: 234 loop : -0.92 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.014 0.001 PHE B 338 TYR 0.014 0.001 TYR B1030 ARG 0.003 0.000 ARG A 513 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 3) link_NAG-ASN : angle 4.66278 ( 9) link_ALPHA1-6 : bond 0.01479 ( 1) link_ALPHA1-6 : angle 2.60467 ( 3) link_BETA1-4 : bond 0.00466 ( 2) link_BETA1-4 : angle 1.47630 ( 6) hydrogen bonds : bond 0.03884 ( 425) hydrogen bonds : angle 4.25462 ( 1197) link_BETA1-6 : bond 0.01198 ( 2) link_BETA1-6 : angle 2.52483 ( 6) SS BOND : bond 0.00386 ( 1) SS BOND : angle 1.31756 ( 2) covalent geometry : bond 0.00296 (11451) covalent geometry : angle 0.51760 (15492) *********************** 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 165 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.8613 (t0) cc_final: 0.8095 (t0) REVERT: B 461 ASP cc_start: 0.8892 (t0) cc_final: 0.8524 (t0) REVERT: B 561 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: B 646 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6804 (pmm) REVERT: B 758 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 884 GLU cc_start: 0.8243 (tt0) cc_final: 0.7948 (mt-10) outliers start: 38 outliers final: 22 residues processed: 154 average time/residue: 0.2279 time to fit residues: 51.8784 Evaluate side-chains 144 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 447 GLN 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 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 561 HIS 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 755 THR Chi-restraints excluded: chain B residue 758 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 996 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** B1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097639 restraints weight = 19599.234| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.73 r_work: 0.3070 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11460 Z= 0.179 Angle : 0.568 11.801 15518 Z= 0.292 Chirality : 0.046 0.424 1721 Planarity : 0.003 0.042 1976 Dihedral : 9.235 109.021 1628 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.04 % Allowed : 23.97 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1345 helix: 2.66 (0.27), residues: 369 sheet: -0.56 (0.32), residues: 238 loop : -0.97 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.022 0.002 PHE A 473 TYR 0.014 0.001 TYR B1030 ARG 0.004 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 3) link_NAG-ASN : angle 4.54040 ( 9) link_ALPHA1-6 : bond 0.01673 ( 1) link_ALPHA1-6 : angle 2.68245 ( 3) link_BETA1-4 : bond 0.00498 ( 2) link_BETA1-4 : angle 1.43183 ( 6) hydrogen bonds : bond 0.04191 ( 425) hydrogen bonds : angle 4.33184 ( 1197) link_BETA1-6 : bond 0.01037 ( 2) link_BETA1-6 : angle 2.48356 ( 6) SS BOND : bond 0.00282 ( 1) SS BOND : angle 1.49417 ( 2) covalent geometry : bond 0.00431 (11451) covalent geometry : angle 0.55369 (15492) *********************** 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 175 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5817 (mptt) REVERT: A 448 ILE cc_start: 0.8168 (pt) cc_final: 0.7825 (mt) REVERT: B 56 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: B 67 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7364 (mp10) REVERT: B 148 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: B 461 ASP cc_start: 0.8942 (t0) cc_final: 0.8564 (t0) REVERT: B 646 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6807 (pmm) REVERT: B 758 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: B 884 GLU cc_start: 0.8283 (tt0) cc_final: 0.7971 (mt-10) REVERT: B 934 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8483 (p90) outliers start: 50 outliers final: 35 residues processed: 161 average time/residue: 0.2294 time to fit residues: 53.9408 Evaluate side-chains 162 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN 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 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 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 531 MET Chi-restraints excluded: chain B residue 561 HIS 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 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 889 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 934 TYR 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 1220 VAL 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 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 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 = 0.3506 r_free = 0.3506 target = 0.119491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098215 restraints weight = 19807.700| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.75 r_work: 0.3082 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11460 Z= 0.152 Angle : 0.555 11.495 15518 Z= 0.283 Chirality : 0.045 0.427 1721 Planarity : 0.003 0.041 1976 Dihedral : 8.749 106.133 1628 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.55 % Allowed : 24.46 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1345 helix: 2.74 (0.27), residues: 368 sheet: -0.53 (0.32), residues: 238 loop : -0.94 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.018 0.001 PHE A 473 TYR 0.014 0.001 TYR B1030 ARG 0.004 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 3) link_NAG-ASN : angle 4.47690 ( 9) link_ALPHA1-6 : bond 0.01978 ( 1) link_ALPHA1-6 : angle 2.48200 ( 3) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.52144 ( 6) hydrogen bonds : bond 0.03994 ( 425) hydrogen bonds : angle 4.27808 ( 1197) link_BETA1-6 : bond 0.01087 ( 2) link_BETA1-6 : angle 2.55457 ( 6) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.40547 ( 2) covalent geometry : bond 0.00360 (11451) covalent geometry : angle 0.54005 (15492) *********************** 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 174 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5895 (mmtt) REVERT: A 448 ILE cc_start: 0.8217 (pt) cc_final: 0.7838 (mt) REVERT: A 501 ASN cc_start: 0.8614 (t0) cc_final: 0.8066 (t0) REVERT: B 67 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7373 (mp10) REVERT: B 148 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: B 461 ASP cc_start: 0.8937 (t0) cc_final: 0.8545 (t0) REVERT: B 561 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: B 646 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6816 (pmm) REVERT: B 758 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: B 879 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 884 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7987 (mt-10) outliers start: 44 outliers final: 31 residues processed: 163 average time/residue: 0.2777 time to fit residues: 68.2645 Evaluate side-chains 162 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU 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 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 531 MET Chi-restraints excluded: chain B residue 561 HIS 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 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 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 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 91 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.120495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099324 restraints weight = 19521.157| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.75 r_work: 0.3097 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11460 Z= 0.127 Angle : 0.542 11.195 15518 Z= 0.277 Chirality : 0.045 0.419 1721 Planarity : 0.003 0.041 1976 Dihedral : 8.113 103.607 1628 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.71 % Allowed : 24.70 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1345 helix: 2.80 (0.27), residues: 369 sheet: -0.44 (0.33), residues: 233 loop : -0.92 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.027 0.001 PHE A 473 TYR 0.017 0.001 TYR B 751 ARG 0.004 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 3) link_NAG-ASN : angle 4.31635 ( 9) link_ALPHA1-6 : bond 0.02210 ( 1) link_ALPHA1-6 : angle 1.32722 ( 3) link_BETA1-4 : bond 0.00537 ( 2) link_BETA1-4 : angle 1.68011 ( 6) hydrogen bonds : bond 0.03794 ( 425) hydrogen bonds : angle 4.20113 ( 1197) link_BETA1-6 : bond 0.01091 ( 2) link_BETA1-6 : angle 2.59276 ( 6) SS BOND : bond 0.00372 ( 1) SS BOND : angle 1.32573 ( 2) covalent geometry : bond 0.00296 (11451) covalent geometry : angle 0.52865 (15492) *********************** 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 174 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5720 (mmtt) REVERT: A 448 ILE cc_start: 0.8234 (pt) cc_final: 0.7851 (mt) REVERT: A 501 ASN cc_start: 0.8667 (t0) cc_final: 0.8076 (t0) REVERT: A 507 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7730 (p-80) REVERT: B 67 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7359 (mp10) REVERT: B 106 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8678 (mtm) REVERT: B 148 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: B 461 ASP cc_start: 0.8925 (t0) cc_final: 0.8539 (t0) REVERT: B 561 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: B 646 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6802 (pmm) REVERT: B 758 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: B 879 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 884 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 934 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8351 (p90) outliers start: 46 outliers final: 32 residues processed: 163 average time/residue: 0.2407 time to fit residues: 57.6623 Evaluate side-chains 164 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 507 HIS 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 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 411 MET 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 561 HIS 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 755 THR Chi-restraints excluded: chain B residue 758 GLU 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 934 TYR 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 Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099028 restraints weight = 19609.716| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.74 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11460 Z= 0.139 Angle : 0.552 11.173 15518 Z= 0.283 Chirality : 0.045 0.415 1721 Planarity : 0.003 0.041 1976 Dihedral : 7.926 102.559 1628 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.79 % Allowed : 25.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1345 helix: 2.68 (0.27), residues: 375 sheet: -0.44 (0.33), residues: 238 loop : -0.90 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1266 HIS 0.005 0.001 HIS B 223 PHE 0.026 0.001 PHE A 473 TYR 0.015 0.001 TYR A 478 ARG 0.006 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 3) link_NAG-ASN : angle 4.24621 ( 9) link_ALPHA1-6 : bond 0.02046 ( 1) link_ALPHA1-6 : angle 1.36181 ( 3) link_BETA1-4 : bond 0.00527 ( 2) link_BETA1-4 : angle 1.80789 ( 6) hydrogen bonds : bond 0.03824 ( 425) hydrogen bonds : angle 4.21332 ( 1197) link_BETA1-6 : bond 0.01066 ( 2) link_BETA1-6 : angle 2.63491 ( 6) SS BOND : bond 0.00338 ( 1) SS BOND : angle 1.34580 ( 2) covalent geometry : bond 0.00327 (11451) covalent geometry : angle 0.53899 (15492) *********************** 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 172 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6375 (OUTLIER) cc_final: 0.5697 (mmtt) REVERT: A 448 ILE cc_start: 0.8237 (pt) cc_final: 0.7875 (mt) REVERT: A 501 ASN cc_start: 0.8653 (t0) cc_final: 0.8098 (t0) REVERT: A 507 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7809 (p-80) REVERT: B 67 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7366 (mp10) REVERT: B 106 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (mtm) REVERT: B 148 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 461 ASP cc_start: 0.8928 (t0) cc_final: 0.8535 (t0) REVERT: B 561 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.7114 (t-90) REVERT: B 646 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6815 (pmm) REVERT: B 758 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 879 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 884 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 934 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8374 (p90) outliers start: 47 outliers final: 32 residues processed: 162 average time/residue: 0.2314 time to fit residues: 54.9440 Evaluate side-chains 163 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 507 HIS 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 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 411 MET 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 561 HIS 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 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 934 TYR 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 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 84 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.118452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097294 restraints weight = 19595.559| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.72 r_work: 0.3064 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11460 Z= 0.204 Angle : 0.601 11.304 15518 Z= 0.310 Chirality : 0.046 0.413 1721 Planarity : 0.003 0.041 1976 Dihedral : 8.036 104.984 1628 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.71 % Allowed : 25.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1345 helix: 2.53 (0.27), residues: 376 sheet: -0.58 (0.32), residues: 240 loop : -1.00 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 717 HIS 0.005 0.001 HIS B 223 PHE 0.029 0.002 PHE A 473 TYR 0.015 0.001 TYR B 751 ARG 0.006 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 3) link_NAG-ASN : angle 4.25342 ( 9) link_ALPHA1-6 : bond 0.01762 ( 1) link_ALPHA1-6 : angle 1.43699 ( 3) link_BETA1-4 : bond 0.00508 ( 2) link_BETA1-4 : angle 1.93068 ( 6) hydrogen bonds : bond 0.04223 ( 425) hydrogen bonds : angle 4.34234 ( 1197) link_BETA1-6 : bond 0.00968 ( 2) link_BETA1-6 : angle 2.84325 ( 6) SS BOND : bond 0.00247 ( 1) SS BOND : angle 1.54827 ( 2) covalent geometry : bond 0.00495 (11451) covalent geometry : angle 0.58854 (15492) ********************** 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 168 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5891 (mmtt) REVERT: A 448 ILE cc_start: 0.8237 (pt) cc_final: 0.7757 (mt) REVERT: A 450 GLN cc_start: 0.7361 (mt0) cc_final: 0.7113 (mm-40) REVERT: A 507 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (p-80) REVERT: B 67 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7412 (mp10) REVERT: B 106 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8726 (mtm) REVERT: B 148 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: B 461 ASP cc_start: 0.8994 (t0) cc_final: 0.8599 (t0) REVERT: B 646 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6824 (pmm) REVERT: B 758 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 879 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 884 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: B 934 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8310 (p90) outliers start: 46 outliers final: 33 residues processed: 159 average time/residue: 0.2413 time to fit residues: 56.6283 Evaluate side-chains 163 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 507 HIS 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 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 411 MET 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 561 HIS 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 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 932 ILE Chi-restraints excluded: chain B residue 934 TYR 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 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 110 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 overall best weight: 0.6216 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.120370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099297 restraints weight = 19446.561| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.72 r_work: 0.3099 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11460 Z= 0.127 Angle : 0.556 10.804 15518 Z= 0.287 Chirality : 0.045 0.408 1721 Planarity : 0.003 0.041 1976 Dihedral : 7.670 102.907 1628 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.55 % Allowed : 25.59 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1345 helix: 2.65 (0.27), residues: 376 sheet: -0.52 (0.32), residues: 240 loop : -0.94 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B1266 HIS 0.004 0.001 HIS B 223 PHE 0.026 0.001 PHE A 473 TYR 0.017 0.001 TYR B 751 ARG 0.006 0.000 ARG B 861 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 3) link_NAG-ASN : angle 4.07422 ( 9) link_ALPHA1-6 : bond 0.01602 ( 1) link_ALPHA1-6 : angle 1.16121 ( 3) link_BETA1-4 : bond 0.00408 ( 2) link_BETA1-4 : angle 2.00327 ( 6) hydrogen bonds : bond 0.03812 ( 425) hydrogen bonds : angle 4.21737 ( 1197) link_BETA1-6 : bond 0.01269 ( 2) link_BETA1-6 : angle 2.73851 ( 6) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.30723 ( 2) covalent geometry : bond 0.00296 (11451) covalent geometry : angle 0.54284 (15492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6856.76 seconds wall clock time: 121 minutes 15.66 seconds (7275.66 seconds total)