Starting phenix.real_space_refine on Sat May 10 01:14:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlg_36396/05_2025/8jlg_36396.cif" } resolution = 2.87 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2829 2.51 5 N 738 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 923 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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 Time building chain proxies: 3.46, per 1000 atoms: 0.78 Number of scatterers: 4426 At special positions: 0 Unit cell: (83.83, 82.17, 92.13, 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 15 16.00 O 844 8.00 N 738 7.00 C 2829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 498 " " NAG A 602 " - " ASN A 548 " " NAG E 1 " - " ASN A 573 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 555.4 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.7% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.758A pdb=" N THR A 484 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.692A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.544A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1091 Processing helix chain 'B' and resid 1210 through 1214 removed outlier: 4.012A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 493 removed outlier: 6.189A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'A' and resid 550 through 552 Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 5.939A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE A 545 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 524 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG A 547 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 526 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 512 current: chain 'A' and resid 555 through 559 Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.581A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 879 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B1072 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.581A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 879 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B1072 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE B1069 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 941 " --> pdb=" O ASN B1021 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900 removed outlier: 7.303A pdb=" N LYS B1052 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 968 " --> pdb=" O LYS B1052 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA7, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA8, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.986A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.061A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.354A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.632A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B1248 " --> pdb=" O LEU B1239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.986A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 402 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: 1.47 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 764 1.32 - 1.45: 1415 1.45 - 1.58: 2317 1.58 - 1.71: 0 1.71 - 1.84: 23 Bond restraints: 4519 Sorted by residual: bond pdb=" C ILE B1161 " pdb=" N ILE B1162 " ideal model delta sigma weight residual 1.330 1.277 0.054 1.26e-02 6.30e+03 1.81e+01 bond pdb=" CA SER B1281 " pdb=" CB SER B1281 " ideal model delta sigma weight residual 1.531 1.466 0.064 1.52e-02 4.33e+03 1.79e+01 bond pdb=" C TYR B1001 " pdb=" O TYR B1001 " ideal model delta sigma weight residual 1.236 1.187 0.048 1.20e-02 6.94e+03 1.62e+01 bond pdb=" C ILE B1029 " pdb=" O ILE B1029 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.02e-02 9.61e+03 1.31e+01 bond pdb=" C GLY B 981 " pdb=" O GLY B 981 " ideal model delta sigma weight residual 1.236 1.190 0.045 1.31e-02 5.83e+03 1.21e+01 ... (remaining 4514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5134 1.46 - 2.91: 849 2.91 - 4.37: 102 4.37 - 5.82: 14 5.82 - 7.28: 7 Bond angle restraints: 6106 Sorted by residual: angle pdb=" CA ASP B1256 " pdb=" CB ASP B1256 " pdb=" CG ASP B1256 " ideal model delta sigma weight residual 112.60 116.45 -3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C PRO B1119 " pdb=" N ASN B1120 " pdb=" CA ASN B1120 " ideal model delta sigma weight residual 122.65 116.95 5.70 1.60e+00 3.91e-01 1.27e+01 angle pdb=" OD1 ASN B1103 " pdb=" CG ASN B1103 " pdb=" ND2 ASN B1103 " ideal model delta sigma weight residual 122.60 126.09 -3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N PRO B1119 " pdb=" CA PRO B1119 " pdb=" CB PRO B1119 " ideal model delta sigma weight residual 102.17 105.77 -3.60 1.05e+00 9.07e-01 1.17e+01 angle pdb=" N ASN B1120 " pdb=" CA ASN B1120 " pdb=" CB ASN B1120 " ideal model delta sigma weight residual 110.56 115.28 -4.72 1.46e+00 4.69e-01 1.04e+01 ... (remaining 6101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 2606 22.70 - 45.39: 112 45.39 - 68.08: 21 68.08 - 90.77: 3 90.77 - 113.47: 3 Dihedral angle restraints: 2745 sinusoidal: 1182 harmonic: 1563 Sorted by residual: dihedral pdb=" CA GLU A 532 " pdb=" C GLU A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE A 499 " pdb=" C PHE A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C1 NAG A 602 " pdb=" C5 NAG A 602 " pdb=" O5 NAG A 602 " pdb=" C4 NAG A 602 " ideal model delta sinusoidal sigma weight residual -64.11 49.36 -113.47 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 637 0.151 - 0.301: 33 0.301 - 0.451: 3 0.451 - 0.602: 0 0.602 - 0.752: 1 Chirality restraints: 674 Sorted by residual: chirality pdb=" C1 FUC E 3 " pdb=" O6 NAG E 1 " pdb=" C2 FUC E 3 " pdb=" O5 FUC E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.62e+01 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 671 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " -0.037 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 573 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 999 " 0.036 2.00e-02 2.50e+03 3.11e-02 1.69e+01 pdb=" CG PHE B 999 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE B 999 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 999 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 999 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE B 999 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 999 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 576 " 0.036 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE A 576 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 576 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 576 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 576 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 576 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 576 " 0.003 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 493 2.75 - 3.29: 4092 3.29 - 3.83: 7101 3.83 - 4.36: 9176 4.36 - 4.90: 15739 Nonbonded interactions: 36601 Sorted by model distance: nonbonded pdb=" OD1 ASN B1216 " pdb=" ND2 ASN B1242 " model vdw 2.213 3.120 nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.215 3.120 nonbonded pdb=" NH2 ARG A 570 " pdb=" O7 NAG A 602 " model vdw 2.262 3.120 nonbonded pdb=" OH TYR B 980 " pdb=" O ILE B1148 " model vdw 2.272 3.040 nonbonded pdb=" ND2 ASN B 918 " pdb=" O ASP B1062 " model vdw 2.304 3.120 ... (remaining 36596 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 14.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.011 0.090 4524 Z= 0.678 Angle : 1.129 10.058 6121 Z= 0.687 Chirality : 0.085 0.752 674 Planarity : 0.009 0.103 775 Dihedral : 13.811 113.467 1745 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.35), residues: 527 helix: 1.04 (1.04), residues: 23 sheet: -0.34 (0.33), residues: 233 loop : -1.07 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.009 TRP B1282 HIS 0.008 0.004 HIS A 506 PHE 0.055 0.012 PHE B 999 TYR 0.040 0.010 TYR B1122 ARG 0.027 0.003 ARG B1175 Details of bonding type rmsd link_NAG-ASN : bond 0.02056 ( 3) link_NAG-ASN : angle 4.83719 ( 9) link_BETA1-4 : bond 0.00684 ( 1) link_BETA1-4 : angle 2.03476 ( 3) hydrogen bonds : bond 0.21344 ( 140) hydrogen bonds : angle 8.52949 ( 402) link_BETA1-6 : bond 0.01229 ( 1) link_BETA1-6 : angle 1.11437 ( 3) covalent geometry : bond 0.01128 ( 4519) covalent geometry : angle 1.11368 ( 6106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.513 Fit side-chains REVERT: B 1000 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8354 (mttp) REVERT: B 1052 LYS cc_start: 0.7817 (mttt) cc_final: 0.7607 (ttmt) REVERT: B 1118 ASP cc_start: 0.6869 (t70) cc_final: 0.6535 (t70) REVERT: B 1130 ILE cc_start: 0.7908 (mp) cc_final: 0.7637 (tp) REVERT: B 1266 TRP cc_start: 0.6567 (t60) cc_final: 0.6314 (t60) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.1843 time to fit residues: 113.1597 Evaluate side-chains 64 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129028 restraints weight = 5032.107| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.44 r_work: 0.3385 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4524 Z= 0.135 Angle : 0.575 10.242 6121 Z= 0.303 Chirality : 0.050 0.378 674 Planarity : 0.003 0.031 775 Dihedral : 9.095 89.611 687 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 11.07 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.35), residues: 527 helix: 1.50 (1.04), residues: 23 sheet: -0.16 (0.34), residues: 220 loop : -0.97 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1266 HIS 0.002 0.000 HIS A 506 PHE 0.016 0.001 PHE A 497 TYR 0.013 0.001 TYR B1149 ARG 0.003 0.000 ARG B1179 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 3) link_NAG-ASN : angle 4.59379 ( 9) link_BETA1-4 : bond 0.00411 ( 1) link_BETA1-4 : angle 1.37300 ( 3) hydrogen bonds : bond 0.03480 ( 140) hydrogen bonds : angle 5.86218 ( 402) link_BETA1-6 : bond 0.00355 ( 1) link_BETA1-6 : angle 1.27546 ( 3) covalent geometry : bond 0.00314 ( 4519) covalent geometry : angle 0.54628 ( 6106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 527 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8695 (mt-10) REVERT: B 1000 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8094 (mttp) REVERT: B 1052 LYS cc_start: 0.8197 (mttt) cc_final: 0.7693 (ttmt) REVERT: B 1118 ASP cc_start: 0.6946 (t70) cc_final: 0.6742 (t70) REVERT: B 1130 ILE cc_start: 0.8470 (mp) cc_final: 0.8112 (tp) REVERT: B 1189 LYS cc_start: 0.7610 (tttt) cc_final: 0.7300 (mtpp) REVERT: B 1190 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6693 (tp30) REVERT: B 1203 GLU cc_start: 0.8581 (mp0) cc_final: 0.8373 (mp0) REVERT: B 1266 TRP cc_start: 0.6519 (t60) cc_final: 0.6312 (t60) outliers start: 10 outliers final: 4 residues processed: 79 average time/residue: 1.2190 time to fit residues: 99.9793 Evaluate side-chains 66 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125036 restraints weight = 5088.799| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.45 r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4524 Z= 0.206 Angle : 0.611 11.120 6121 Z= 0.317 Chirality : 0.051 0.384 674 Planarity : 0.004 0.033 775 Dihedral : 8.459 83.738 687 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.28 % Allowed : 13.52 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.35), residues: 527 helix: 1.40 (1.04), residues: 23 sheet: -0.20 (0.33), residues: 232 loop : -1.16 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 974 HIS 0.002 0.001 HIS A 494 PHE 0.015 0.002 PHE A 497 TYR 0.013 0.002 TYR B 962 ARG 0.006 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 3) link_NAG-ASN : angle 4.50560 ( 9) link_BETA1-4 : bond 0.00402 ( 1) link_BETA1-4 : angle 1.44666 ( 3) hydrogen bonds : bond 0.03512 ( 140) hydrogen bonds : angle 5.49353 ( 402) link_BETA1-6 : bond 0.00326 ( 1) link_BETA1-6 : angle 1.27101 ( 3) covalent geometry : bond 0.00505 ( 4519) covalent geometry : angle 0.58562 ( 6106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.486 Fit side-chains REVERT: A 517 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8485 (pp) REVERT: B 1118 ASP cc_start: 0.7018 (t70) cc_final: 0.6804 (t70) REVERT: B 1130 ILE cc_start: 0.8507 (mp) cc_final: 0.8103 (tp) REVERT: B 1189 LYS cc_start: 0.7556 (tttt) cc_final: 0.7247 (mtpp) REVERT: B 1190 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6834 (tp30) REVERT: B 1266 TRP cc_start: 0.6476 (t60) cc_final: 0.6254 (t60) outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 1.2104 time to fit residues: 94.3826 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN B1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126854 restraints weight = 5041.132| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.44 r_work: 0.3314 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4524 Z= 0.135 Angle : 0.562 11.645 6121 Z= 0.291 Chirality : 0.048 0.327 674 Planarity : 0.003 0.025 775 Dihedral : 7.583 73.283 687 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.87 % Allowed : 16.80 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 527 helix: 1.72 (1.07), residues: 23 sheet: -0.21 (0.35), residues: 220 loop : -0.85 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1266 HIS 0.001 0.000 HIS A 494 PHE 0.046 0.002 PHE A 497 TYR 0.011 0.001 TYR B1149 ARG 0.004 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 4.28736 ( 9) link_BETA1-4 : bond 0.00518 ( 1) link_BETA1-4 : angle 1.31476 ( 3) hydrogen bonds : bond 0.02976 ( 140) hydrogen bonds : angle 5.18451 ( 402) link_BETA1-6 : bond 0.00383 ( 1) link_BETA1-6 : angle 1.23099 ( 3) covalent geometry : bond 0.00323 ( 4519) covalent geometry : angle 0.53702 ( 6106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.510 Fit side-chains REVERT: A 512 PHE cc_start: 0.7741 (t80) cc_final: 0.7485 (t80) REVERT: A 517 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8493 (pp) REVERT: A 532 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: B 911 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7491 (ttmm) REVERT: B 1052 LYS cc_start: 0.8058 (mttt) cc_final: 0.7506 (ttmt) REVERT: B 1130 ILE cc_start: 0.8503 (mp) cc_final: 0.8085 (tp) REVERT: B 1189 LYS cc_start: 0.7494 (tttt) cc_final: 0.7194 (mtpp) REVERT: B 1190 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: B 1266 TRP cc_start: 0.6452 (t60) cc_final: 0.6205 (t60) outliers start: 14 outliers final: 6 residues processed: 73 average time/residue: 1.1694 time to fit residues: 88.7370 Evaluate side-chains 68 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126970 restraints weight = 5115.079| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.46 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4524 Z= 0.130 Angle : 0.549 11.265 6121 Z= 0.283 Chirality : 0.047 0.173 674 Planarity : 0.003 0.024 775 Dihedral : 5.991 36.028 687 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.48 % Allowed : 16.60 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.35), residues: 527 helix: 1.81 (1.06), residues: 23 sheet: -0.08 (0.34), residues: 220 loop : -1.02 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1266 HIS 0.001 0.000 HIS A 494 PHE 0.033 0.002 PHE A 497 TYR 0.011 0.001 TYR B1149 ARG 0.003 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 3) link_NAG-ASN : angle 4.55535 ( 9) link_BETA1-4 : bond 0.00506 ( 1) link_BETA1-4 : angle 1.29598 ( 3) hydrogen bonds : bond 0.02879 ( 140) hydrogen bonds : angle 4.99589 ( 402) link_BETA1-6 : bond 0.00457 ( 1) link_BETA1-6 : angle 1.24286 ( 3) covalent geometry : bond 0.00310 ( 4519) covalent geometry : angle 0.51946 ( 6106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.521 Fit side-chains REVERT: A 512 PHE cc_start: 0.7761 (t80) cc_final: 0.7497 (t80) REVERT: A 517 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 532 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: B 1023 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.7053 (mmt90) REVERT: B 1130 ILE cc_start: 0.8500 (mp) cc_final: 0.8088 (tp) REVERT: B 1189 LYS cc_start: 0.7477 (tttt) cc_final: 0.7180 (mtpp) REVERT: B 1190 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: B 1225 SER cc_start: 0.8483 (t) cc_final: 0.7939 (m) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 1.1268 time to fit residues: 89.0904 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123542 restraints weight = 5038.466| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.44 r_work: 0.3289 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4524 Z= 0.246 Angle : 0.627 10.329 6121 Z= 0.328 Chirality : 0.050 0.157 674 Planarity : 0.004 0.033 775 Dihedral : 5.814 36.478 687 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.69 % Allowed : 17.01 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.34), residues: 527 helix: 1.31 (1.03), residues: 23 sheet: 0.20 (0.41), residues: 146 loop : -1.30 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1266 HIS 0.002 0.001 HIS A 494 PHE 0.030 0.002 PHE A 497 TYR 0.014 0.002 TYR B 962 ARG 0.004 0.000 ARG B1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 3) link_NAG-ASN : angle 4.28601 ( 9) link_BETA1-4 : bond 0.00202 ( 1) link_BETA1-4 : angle 1.50186 ( 3) hydrogen bonds : bond 0.03342 ( 140) hydrogen bonds : angle 5.24274 ( 402) link_BETA1-6 : bond 0.00273 ( 1) link_BETA1-6 : angle 1.32357 ( 3) covalent geometry : bond 0.00604 ( 4519) covalent geometry : angle 0.60443 ( 6106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.635 Fit side-chains REVERT: A 512 PHE cc_start: 0.7788 (t80) cc_final: 0.7520 (t80) REVERT: A 517 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (pt) REVERT: A 532 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: B 1189 LYS cc_start: 0.7512 (tttt) cc_final: 0.7182 (mtpp) REVERT: B 1190 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: B 1210 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 1225 SER cc_start: 0.8519 (t) cc_final: 0.7964 (m) outliers start: 18 outliers final: 10 residues processed: 72 average time/residue: 1.1425 time to fit residues: 85.6599 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1210 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127469 restraints weight = 5029.453| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.42 r_work: 0.3344 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4524 Z= 0.103 Angle : 0.505 10.034 6121 Z= 0.271 Chirality : 0.046 0.170 674 Planarity : 0.003 0.030 775 Dihedral : 5.441 34.314 687 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.28 % Allowed : 18.44 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.35), residues: 527 helix: 1.56 (1.01), residues: 23 sheet: -0.17 (0.34), residues: 226 loop : -1.03 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1266 HIS 0.001 0.000 HIS B1253 PHE 0.025 0.001 PHE A 497 TYR 0.010 0.001 TYR B1001 ARG 0.008 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 3) link_NAG-ASN : angle 3.03180 ( 9) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 1.19781 ( 3) hydrogen bonds : bond 0.02692 ( 140) hydrogen bonds : angle 4.88728 ( 402) link_BETA1-6 : bond 0.00425 ( 1) link_BETA1-6 : angle 1.21903 ( 3) covalent geometry : bond 0.00240 ( 4519) covalent geometry : angle 0.49103 ( 6106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.533 Fit side-chains REVERT: A 570 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: B 911 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7367 (ttmm) REVERT: B 1056 LYS cc_start: 0.7789 (tttt) cc_final: 0.7528 (pttp) REVERT: B 1130 ILE cc_start: 0.8380 (mp) cc_final: 0.7992 (tp) REVERT: B 1189 LYS cc_start: 0.7440 (tttt) cc_final: 0.7144 (mtpp) REVERT: B 1190 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: B 1225 SER cc_start: 0.8443 (t) cc_final: 0.7905 (m) outliers start: 16 outliers final: 8 residues processed: 74 average time/residue: 1.2802 time to fit residues: 98.1862 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124897 restraints weight = 5046.266| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.43 r_work: 0.3286 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4524 Z= 0.174 Angle : 0.560 11.373 6121 Z= 0.297 Chirality : 0.048 0.158 674 Planarity : 0.003 0.027 775 Dihedral : 5.371 35.046 687 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 18.44 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.34), residues: 527 helix: 1.46 (1.01), residues: 23 sheet: 0.29 (0.42), residues: 145 loop : -1.16 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1266 HIS 0.002 0.001 HIS A 494 PHE 0.025 0.002 PHE A 497 TYR 0.012 0.001 TYR B1149 ARG 0.005 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 3) link_NAG-ASN : angle 3.17982 ( 9) link_BETA1-4 : bond 0.00384 ( 1) link_BETA1-4 : angle 1.38268 ( 3) hydrogen bonds : bond 0.02943 ( 140) hydrogen bonds : angle 5.00891 ( 402) link_BETA1-6 : bond 0.00360 ( 1) link_BETA1-6 : angle 1.21671 ( 3) covalent geometry : bond 0.00421 ( 4519) covalent geometry : angle 0.54621 ( 6106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.541 Fit side-chains REVERT: A 517 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8711 (pt) REVERT: A 532 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 570 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7890 (mtm-85) REVERT: B 1130 ILE cc_start: 0.8448 (mp) cc_final: 0.8009 (tp) REVERT: B 1189 LYS cc_start: 0.7488 (tttt) cc_final: 0.7185 (mtpp) REVERT: B 1190 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: B 1203 GLU cc_start: 0.8781 (mp0) cc_final: 0.8471 (mt-10) REVERT: B 1225 SER cc_start: 0.8463 (t) cc_final: 0.7934 (m) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 1.2397 time to fit residues: 95.1666 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126778 restraints weight = 5033.968| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.46 r_work: 0.3330 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4524 Z= 0.118 Angle : 0.504 11.114 6121 Z= 0.270 Chirality : 0.047 0.163 674 Planarity : 0.003 0.026 775 Dihedral : 5.176 33.589 687 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.07 % Allowed : 18.85 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.35), residues: 527 helix: 1.63 (1.01), residues: 23 sheet: -0.21 (0.35), residues: 212 loop : -0.74 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1266 HIS 0.001 0.000 HIS A 494 PHE 0.023 0.002 PHE A 497 TYR 0.010 0.001 TYR B1149 ARG 0.006 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 3) link_NAG-ASN : angle 2.77700 ( 9) link_BETA1-4 : bond 0.00545 ( 1) link_BETA1-4 : angle 1.26524 ( 3) hydrogen bonds : bond 0.02714 ( 140) hydrogen bonds : angle 4.85885 ( 402) link_BETA1-6 : bond 0.00412 ( 1) link_BETA1-6 : angle 1.22783 ( 3) covalent geometry : bond 0.00277 ( 4519) covalent geometry : angle 0.49141 ( 6106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.520 Fit side-chains REVERT: A 517 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (pt) REVERT: A 532 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: A 570 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7885 (mtm-85) REVERT: B 1064 ARG cc_start: 0.7312 (mmp-170) cc_final: 0.7016 (mmp80) REVERT: B 1130 ILE cc_start: 0.8424 (mp) cc_final: 0.7997 (tp) REVERT: B 1189 LYS cc_start: 0.7486 (tttt) cc_final: 0.7196 (mtpp) REVERT: B 1190 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: B 1203 GLU cc_start: 0.8782 (mp0) cc_final: 0.8501 (mt-10) REVERT: B 1225 SER cc_start: 0.8428 (t) cc_final: 0.7924 (m) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 1.2439 time to fit residues: 86.6445 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126196 restraints weight = 4992.527| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.41 r_work: 0.3327 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4524 Z= 0.144 Angle : 0.524 11.756 6121 Z= 0.280 Chirality : 0.047 0.162 674 Planarity : 0.003 0.025 775 Dihedral : 5.129 33.331 687 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.28 % Allowed : 18.65 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.35), residues: 527 helix: 1.58 (1.01), residues: 23 sheet: -0.24 (0.34), residues: 221 loop : -0.75 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1266 HIS 0.001 0.000 HIS A 506 PHE 0.023 0.002 PHE A 497 TYR 0.011 0.001 TYR B1149 ARG 0.005 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 3) link_NAG-ASN : angle 2.77896 ( 9) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 1.31781 ( 3) hydrogen bonds : bond 0.02820 ( 140) hydrogen bonds : angle 4.87891 ( 402) link_BETA1-6 : bond 0.00373 ( 1) link_BETA1-6 : angle 1.21008 ( 3) covalent geometry : bond 0.00346 ( 4519) covalent geometry : angle 0.51252 ( 6106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.489 Fit side-chains REVERT: A 517 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8715 (pt) REVERT: A 532 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: B 1130 ILE cc_start: 0.8431 (mp) cc_final: 0.8027 (tp) REVERT: B 1189 LYS cc_start: 0.7484 (tttt) cc_final: 0.7191 (mtpp) REVERT: B 1190 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: B 1203 GLU cc_start: 0.8765 (mp0) cc_final: 0.8473 (mt-10) REVERT: B 1225 SER cc_start: 0.8408 (t) cc_final: 0.7884 (m) outliers start: 16 outliers final: 11 residues processed: 67 average time/residue: 1.1900 time to fit residues: 82.9526 Evaluate side-chains 72 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1190 GLU Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127563 restraints weight = 5071.437| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.44 r_work: 0.3325 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4524 Z= 0.108 Angle : 0.497 12.059 6121 Z= 0.265 Chirality : 0.046 0.173 674 Planarity : 0.003 0.035 775 Dihedral : 4.946 32.248 687 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.07 % Allowed : 18.44 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.36), residues: 527 helix: 1.74 (1.01), residues: 23 sheet: -0.13 (0.35), residues: 219 loop : -0.74 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1266 HIS 0.001 0.000 HIS A 506 PHE 0.022 0.001 PHE A 497 TYR 0.010 0.001 TYR B1001 ARG 0.008 0.000 ARG A 570 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 3) link_NAG-ASN : angle 2.54532 ( 9) link_BETA1-4 : bond 0.00548 ( 1) link_BETA1-4 : angle 1.23518 ( 3) hydrogen bonds : bond 0.02677 ( 140) hydrogen bonds : angle 4.73638 ( 402) link_BETA1-6 : bond 0.00380 ( 1) link_BETA1-6 : angle 1.21622 ( 3) covalent geometry : bond 0.00253 ( 4519) covalent geometry : angle 0.48618 ( 6106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.22 seconds wall clock time: 69 minutes 15.34 seconds (4155.34 seconds total)