Starting phenix.real_space_refine on Fri Aug 22 14:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlg_36396/08_2025/8jlg_36396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlg_36396/08_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_36396/08_2025/8jlg_36396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlg_36396/08_2025/8jlg_36396.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlg_36396/08_2025/8jlg_36396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlg_36396/08_2025/8jlg_36396.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.84, per 1000 atoms: 0.19 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: 0.39 Conformation dependent library (CDL) restraints added in 161.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.47 Time building geometry restraints manager: 0.51 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: 1.590 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.930 Find NCS groups from input model: 0.080 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.027 0.003 ARG B1175 TYR 0.040 0.010 TYR B1122 PHE 0.055 0.012 PHE B 999 TRP 0.032 0.009 TRP B1282 HIS 0.008 0.004 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.01128 ( 4519) covalent geometry : angle 1.11368 ( 6106) hydrogen bonds : bond 0.21344 ( 140) hydrogen bonds : angle 8.52949 ( 402) link_BETA1-4 : bond 0.00684 ( 1) link_BETA1-4 : angle 2.03476 ( 3) link_BETA1-6 : bond 0.01229 ( 1) link_BETA1-6 : angle 1.11437 ( 3) link_NAG-ASN : bond 0.02056 ( 3) link_NAG-ASN : angle 4.83719 ( 9) *********************** 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 : 0.123 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: 0.5112 time to fit residues: 48.7828 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 : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 30 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: 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 = 0.3922 r_free = 0.3922 target = 0.166182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127552 restraints weight = 5129.887| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.52 r_work: 0.3329 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4524 Z= 0.150 Angle : 0.588 10.757 6121 Z= 0.312 Chirality : 0.050 0.388 674 Planarity : 0.003 0.031 775 Dihedral : 9.356 92.271 687 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 10.66 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.35), residues: 527 helix: 1.42 (1.03), residues: 23 sheet: -0.15 (0.34), residues: 220 loop : -1.01 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 570 TYR 0.012 0.001 TYR B1149 PHE 0.015 0.002 PHE A 497 TRP 0.012 0.002 TRP B 974 HIS 0.001 0.000 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4519) covalent geometry : angle 0.55826 ( 6106) hydrogen bonds : bond 0.04080 ( 140) hydrogen bonds : angle 6.04671 ( 402) link_BETA1-4 : bond 0.00395 ( 1) link_BETA1-4 : angle 1.47857 ( 3) link_BETA1-6 : bond 0.00455 ( 1) link_BETA1-6 : angle 1.12139 ( 3) link_NAG-ASN : bond 0.00753 ( 3) link_NAG-ASN : angle 4.75504 ( 9) *********************** 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 80 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 1052 LYS cc_start: 0.8164 (mttt) cc_final: 0.7647 (ttmt) REVERT: B 1118 ASP cc_start: 0.6996 (t70) cc_final: 0.6777 (t70) REVERT: B 1130 ILE cc_start: 0.8458 (mp) cc_final: 0.8086 (tp) REVERT: B 1189 LYS cc_start: 0.7570 (tttt) cc_final: 0.7289 (mtpp) REVERT: B 1190 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6655 (tp30) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.5729 time to fit residues: 45.5538 Evaluate side-chains 66 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 942 SER 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 33 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 B1270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123987 restraints weight = 5120.476| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.45 r_work: 0.3242 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4524 Z= 0.231 Angle : 0.649 10.975 6121 Z= 0.337 Chirality : 0.053 0.390 674 Planarity : 0.004 0.042 775 Dihedral : 8.647 85.370 687 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.07 % Allowed : 13.93 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.34), residues: 527 helix: 0.67 (0.96), residues: 23 sheet: 0.36 (0.41), residues: 148 loop : -1.33 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.015 0.002 TYR B 962 PHE 0.015 0.002 PHE A 497 TRP 0.038 0.003 TRP B1266 HIS 0.001 0.000 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 4519) covalent geometry : angle 0.62237 ( 6106) hydrogen bonds : bond 0.03739 ( 140) hydrogen bonds : angle 5.61952 ( 402) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 1.44639 ( 3) link_BETA1-6 : bond 0.00269 ( 1) link_BETA1-6 : angle 1.32907 ( 3) link_NAG-ASN : bond 0.00724 ( 3) link_NAG-ASN : angle 4.68474 ( 9) *********************** 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 76 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.177 Fit side-chains REVERT: A 517 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8474 (pp) REVERT: A 532 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: B 1118 ASP cc_start: 0.7074 (t70) cc_final: 0.6858 (t70) REVERT: B 1130 ILE cc_start: 0.8500 (mp) cc_final: 0.8096 (tp) REVERT: B 1189 LYS cc_start: 0.7569 (tttt) cc_final: 0.7256 (mtpp) REVERT: B 1190 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6782 (tp30) outliers start: 15 outliers final: 9 residues processed: 70 average time/residue: 0.4959 time to fit residues: 36.2027 Evaluate side-chains 71 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 5 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: 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 = 0.3905 r_free = 0.3905 target = 0.164695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126736 restraints weight = 5013.095| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.45 r_work: 0.3331 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1776 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= 0.124 Angle : 0.566 11.480 6121 Z= 0.295 Chirality : 0.048 0.340 674 Planarity : 0.003 0.024 775 Dihedral : 7.748 75.963 687 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.46 % Allowed : 17.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.35), residues: 527 helix: 0.92 (0.95), residues: 23 sheet: -0.21 (0.33), residues: 236 loop : -0.97 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.011 0.001 TYR B1149 PHE 0.043 0.002 PHE A 497 TRP 0.011 0.001 TRP B1266 HIS 0.001 0.000 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4519) covalent geometry : angle 0.54100 ( 6106) hydrogen bonds : bond 0.03020 ( 140) hydrogen bonds : angle 5.23031 ( 402) link_BETA1-4 : bond 0.00647 ( 1) link_BETA1-4 : angle 1.30150 ( 3) link_BETA1-6 : bond 0.00518 ( 1) link_BETA1-6 : angle 1.29131 ( 3) link_NAG-ASN : bond 0.00622 ( 3) link_NAG-ASN : angle 4.29232 ( 9) *********************** 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 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.186 Fit side-chains REVERT: A 532 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: B 911 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7400 (ttmm) REVERT: B 1130 ILE cc_start: 0.8496 (mp) cc_final: 0.8094 (tp) REVERT: B 1189 LYS cc_start: 0.7544 (tttt) cc_final: 0.7263 (mtpp) REVERT: B 1225 SER cc_start: 0.8512 (t) cc_final: 0.7943 (m) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.4778 time to fit residues: 34.8270 Evaluate side-chains 66 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127055 restraints weight = 5068.833| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.44 r_work: 0.3316 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.003 0.029 4524 Z= 0.127 Angle : 0.561 11.128 6121 Z= 0.289 Chirality : 0.047 0.192 674 Planarity : 0.003 0.024 775 Dihedral : 6.337 46.463 687 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.28 % Allowed : 17.62 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.35), residues: 527 helix: 1.43 (1.00), residues: 23 sheet: -0.12 (0.35), residues: 216 loop : -0.84 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.011 0.001 TYR B1149 PHE 0.034 0.002 PHE A 497 TRP 0.010 0.001 TRP B 974 HIS 0.002 0.001 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4519) covalent geometry : angle 0.53330 ( 6106) hydrogen bonds : bond 0.02902 ( 140) hydrogen bonds : angle 5.04561 ( 402) link_BETA1-4 : bond 0.00534 ( 1) link_BETA1-4 : angle 1.31071 ( 3) link_BETA1-6 : bond 0.00433 ( 1) link_BETA1-6 : angle 1.21524 ( 3) link_NAG-ASN : bond 0.00513 ( 3) link_NAG-ASN : angle 4.44410 ( 9) *********************** 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 81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.117 Fit side-chains REVERT: A 517 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 1023 ARG cc_start: 0.7362 (mmm-85) cc_final: 0.7049 (mmt90) REVERT: B 1130 ILE cc_start: 0.8500 (mp) cc_final: 0.8091 (tp) REVERT: B 1189 LYS cc_start: 0.7526 (tttt) cc_final: 0.7253 (mtpp) REVERT: B 1190 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6745 (tp30) REVERT: B 1225 SER cc_start: 0.8468 (t) cc_final: 0.7913 (m) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.5034 time to fit residues: 39.1507 Evaluate side-chains 68 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 517 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.162266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124437 restraints weight = 5121.357| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.45 r_work: 0.3299 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1940 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= 0.200 Angle : 0.592 9.485 6121 Z= 0.312 Chirality : 0.048 0.161 674 Planarity : 0.004 0.028 775 Dihedral : 5.747 36.569 687 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 17.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.35), residues: 527 helix: 1.41 (1.02), residues: 23 sheet: -0.24 (0.33), residues: 230 loop : -1.11 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 570 TYR 0.013 0.001 TYR B1149 PHE 0.029 0.002 PHE A 497 TRP 0.012 0.002 TRP B 974 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 4519) covalent geometry : angle 0.57092 ( 6106) hydrogen bonds : bond 0.03197 ( 140) hydrogen bonds : angle 5.18359 ( 402) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 1.40651 ( 3) link_BETA1-6 : bond 0.00368 ( 1) link_BETA1-6 : angle 1.28919 ( 3) link_NAG-ASN : bond 0.00527 ( 3) link_NAG-ASN : angle 3.99615 ( 9) *********************** 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 77 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.115 Fit side-chains REVERT: A 517 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8713 (pt) REVERT: A 570 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: B 911 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7378 (ttmm) REVERT: B 1189 LYS cc_start: 0.7542 (tttt) cc_final: 0.7261 (mtpp) REVERT: B 1190 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: B 1225 SER cc_start: 0.8504 (t) cc_final: 0.7947 (m) REVERT: B 1227 ASP cc_start: 0.6023 (m-30) cc_final: 0.5803 (m-30) REVERT: B 1266 TRP cc_start: 0.6874 (t60) cc_final: 0.6462 (t60) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.5446 time to fit residues: 40.0793 Evaluate side-chains 68 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.163999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126348 restraints weight = 5119.563| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.45 r_work: 0.3290 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2069 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= 0.125 Angle : 0.525 10.280 6121 Z= 0.280 Chirality : 0.047 0.167 674 Planarity : 0.003 0.027 775 Dihedral : 5.490 35.374 687 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.48 % Allowed : 17.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.35), residues: 527 helix: 1.72 (1.04), residues: 23 sheet: -0.21 (0.34), residues: 222 loop : -0.84 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 570 TYR 0.011 0.001 TYR B1149 PHE 0.026 0.002 PHE A 497 TRP 0.010 0.001 TRP B 974 HIS 0.001 0.001 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4519) covalent geometry : angle 0.50934 ( 6106) hydrogen bonds : bond 0.02792 ( 140) hydrogen bonds : angle 4.96050 ( 402) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 1.29720 ( 3) link_BETA1-6 : bond 0.00352 ( 1) link_BETA1-6 : angle 1.20671 ( 3) link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 3.19546 ( 9) *********************** 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: 17 poor density : 63 time to evaluate : 0.203 Fit side-chains REVERT: A 517 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8693 (pt) REVERT: A 532 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: A 570 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7906 (mtm-85) REVERT: B 911 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7387 (ttmm) REVERT: B 1056 LYS cc_start: 0.7690 (tttt) cc_final: 0.7399 (pttp) REVERT: B 1130 ILE cc_start: 0.8372 (mp) cc_final: 0.7990 (tp) REVERT: B 1189 LYS cc_start: 0.7466 (tttt) cc_final: 0.7180 (mtpp) REVERT: B 1190 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: B 1225 SER cc_start: 0.8425 (t) cc_final: 0.7881 (m) REVERT: B 1227 ASP cc_start: 0.6022 (m-30) cc_final: 0.5791 (m-30) REVERT: B 1266 TRP cc_start: 0.6829 (t60) cc_final: 0.6430 (t60) outliers start: 17 outliers final: 11 residues processed: 75 average time/residue: 0.5717 time to fit residues: 44.5389 Evaluate side-chains 76 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.165329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127601 restraints weight = 5048.450| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.46 r_work: 0.3343 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4524 Z= 0.109 Angle : 0.503 11.314 6121 Z= 0.269 Chirality : 0.047 0.167 674 Planarity : 0.003 0.025 775 Dihedral : 5.107 34.067 687 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.07 % Allowed : 18.03 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.35), residues: 527 helix: 1.96 (1.06), residues: 23 sheet: 0.25 (0.43), residues: 142 loop : -0.84 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 570 TYR 0.010 0.001 TYR B1149 PHE 0.024 0.001 PHE A 497 TRP 0.009 0.001 TRP B 974 HIS 0.002 0.001 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4519) covalent geometry : angle 0.49083 ( 6106) hydrogen bonds : bond 0.02682 ( 140) hydrogen bonds : angle 4.78827 ( 402) link_BETA1-4 : bond 0.00653 ( 1) link_BETA1-4 : angle 1.26254 ( 3) link_BETA1-6 : bond 0.00411 ( 1) link_BETA1-6 : angle 1.21186 ( 3) link_NAG-ASN : bond 0.00460 ( 3) link_NAG-ASN : angle 2.69938 ( 9) *********************** 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 78 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.221 Fit side-chains REVERT: A 517 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8503 (pp) REVERT: A 532 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 570 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: B 911 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7444 (ttmm) REVERT: B 1056 LYS cc_start: 0.7800 (tttt) cc_final: 0.7521 (pttp) REVERT: B 1064 ARG cc_start: 0.7283 (mmp-170) cc_final: 0.6980 (mmp80) REVERT: B 1130 ILE cc_start: 0.8437 (mp) cc_final: 0.8034 (tp) REVERT: B 1189 LYS cc_start: 0.7497 (tttt) cc_final: 0.7227 (mtpp) REVERT: B 1190 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: B 1225 SER cc_start: 0.8405 (t) cc_final: 0.7884 (m) REVERT: B 1266 TRP cc_start: 0.6853 (t60) cc_final: 0.6424 (t60) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.5387 time to fit residues: 39.7431 Evaluate side-chains 75 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 1209 LEU 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 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 = 0.162578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124550 restraints weight = 5124.140| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.46 r_work: 0.3166 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4524 Z= 0.196 Angle : 0.573 10.313 6121 Z= 0.304 Chirality : 0.049 0.161 674 Planarity : 0.003 0.026 775 Dihedral : 5.316 34.174 687 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.07 % Allowed : 18.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.34), residues: 527 helix: 1.70 (1.03), residues: 23 sheet: 0.15 (0.42), residues: 141 loop : -1.01 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 570 TYR 0.013 0.001 TYR B1149 PHE 0.024 0.002 PHE A 497 TRP 0.011 0.001 TRP B 974 HIS 0.004 0.001 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4519) covalent geometry : angle 0.55916 ( 6106) hydrogen bonds : bond 0.03073 ( 140) hydrogen bonds : angle 5.05973 ( 402) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 1.41486 ( 3) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.24234 ( 3) link_NAG-ASN : bond 0.00493 ( 3) link_NAG-ASN : angle 3.10155 ( 9) *********************** 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 76 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.109 Fit side-chains REVERT: A 517 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8641 (pt) REVERT: A 532 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: B 925 GLU cc_start: 0.7627 (tp30) cc_final: 0.6997 (tp30) REVERT: B 1056 LYS cc_start: 0.7686 (tttt) cc_final: 0.7368 (pttp) REVERT: B 1130 ILE cc_start: 0.8349 (mp) cc_final: 0.7925 (tp) REVERT: B 1189 LYS cc_start: 0.7389 (tttt) cc_final: 0.7094 (mtpp) REVERT: B 1190 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6691 (tp30) REVERT: B 1225 SER cc_start: 0.8379 (t) cc_final: 0.7812 (m) REVERT: B 1266 TRP cc_start: 0.6786 (t60) cc_final: 0.6269 (t60) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.5375 time to fit residues: 40.0674 Evaluate side-chains 72 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.163119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125160 restraints weight = 5058.284| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.48 r_work: 0.3311 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4524 Z= 0.159 Angle : 0.541 11.647 6121 Z= 0.288 Chirality : 0.048 0.164 674 Planarity : 0.003 0.025 775 Dihedral : 5.257 33.264 687 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.87 % Allowed : 18.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.35), residues: 527 helix: 1.82 (1.04), residues: 23 sheet: -0.32 (0.33), residues: 230 loop : -0.93 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 570 TYR 0.011 0.001 TYR B1149 PHE 0.023 0.002 PHE A 497 TRP 0.011 0.001 TRP B 974 HIS 0.003 0.001 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4519) covalent geometry : angle 0.52849 ( 6106) hydrogen bonds : bond 0.02886 ( 140) hydrogen bonds : angle 4.99534 ( 402) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 1.33183 ( 3) link_BETA1-6 : bond 0.00334 ( 1) link_BETA1-6 : angle 1.23994 ( 3) link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 2.90596 ( 9) ********************** 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 73 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.157 Fit side-chains REVERT: A 517 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8737 (pt) REVERT: A 532 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: B 925 GLU cc_start: 0.7727 (tp30) cc_final: 0.7121 (tp30) REVERT: B 1130 ILE cc_start: 0.8428 (mp) cc_final: 0.8005 (tp) REVERT: B 1189 LYS cc_start: 0.7512 (tttt) cc_final: 0.7238 (mtpp) REVERT: B 1190 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6699 (tp30) REVERT: B 1225 SER cc_start: 0.8412 (t) cc_final: 0.7899 (m) REVERT: B 1266 TRP cc_start: 0.6872 (t60) cc_final: 0.6355 (t60) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.4919 time to fit residues: 34.6713 Evaluate side-chains 70 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 544 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.0050 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 overall best weight: 0.4512 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128901 restraints weight = 5043.344| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.43 r_work: 0.3360 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4524 Z= 0.100 Angle : 0.487 12.205 6121 Z= 0.261 Chirality : 0.046 0.172 674 Planarity : 0.002 0.025 775 Dihedral : 4.904 31.629 687 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.66 % Allowed : 19.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.36), residues: 527 helix: 2.24 (1.07), residues: 23 sheet: -0.17 (0.36), residues: 215 loop : -0.72 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 570 TYR 0.010 0.001 TYR B1149 PHE 0.021 0.001 PHE A 497 TRP 0.009 0.001 TRP B 985 HIS 0.001 0.000 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4519) covalent geometry : angle 0.47708 ( 6106) hydrogen bonds : bond 0.02569 ( 140) hydrogen bonds : angle 4.71753 ( 402) link_BETA1-4 : bond 0.00668 ( 1) link_BETA1-4 : angle 1.23471 ( 3) link_BETA1-6 : bond 0.00387 ( 1) link_BETA1-6 : angle 1.22184 ( 3) link_NAG-ASN : bond 0.00419 ( 3) link_NAG-ASN : angle 2.39461 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.63 seconds wall clock time: 31 minutes 35.94 seconds (1895.94 seconds total)