Starting phenix.real_space_refine on Mon Jul 28 01:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801.map" model { file = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2025/7q4c_13801_trim.cif" } resolution = 4.08 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= 0.003 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 24 5.16 5 Cl 1 4.86 5 C 3133 2.51 5 N 822 2.21 5 O 925 1.98 5 H 4598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9503 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 9368 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 551} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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 Chain: "D" 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 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.29, per 1000 atoms: 0.56 Number of scatterers: 9503 At special positions: 0 Unit cell: (78.44, 79.5, 81.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 24 16.00 O 925 8.00 N 822 7.00 C 3133 6.00 H 4598 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 928 " - pdb=" SG CYS A 946 " distance=2.03 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A3002 " - " ASN A 666 " " NAG A3003 " - " ASN A 913 " " NAG B 1 " - " ASN A 648 " " NAG C 1 " - " ASN A 685 " " NAG D 1 " - " ASN A 731 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 622.0 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 71.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 617 through 648 removed outlier: 4.034A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 removed outlier: 3.581A pdb=" N SER A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 678 No H-bonds generated for 'chain 'A' and resid 677 through 678' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.705A pdb=" N GLN A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 725 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.845A pdb=" N ARG A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.871A pdb=" N MET A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 836 removed outlier: 3.614A pdb=" N LEU A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 818 - end of helix Processing helix chain 'A' and resid 859 through 861 No H-bonds generated for 'chain 'A' and resid 859 through 861' Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 902 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 950 through 970 Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.719A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 990 " --> pdb=" O HIS A 986 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1006 Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.802A pdb=" N ASP A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 3.897A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1070 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1096 through 1118 removed outlier: 3.799A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.775A pdb=" N GLN A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 4.146A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'A' and resid 1172 through 1186 Processing sheet with id=AA1, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.257A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 931 through 934 276 hydrogen bonds defined for protein. 789 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: 3.22 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4597 1.03 - 1.23: 7 1.23 - 1.42: 2169 1.42 - 1.62: 2829 1.62 - 1.81: 41 Bond restraints: 9643 Sorted by residual: bond pdb=" C1 NAG A3002 " pdb=" O5 NAG A3002 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.95e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 9638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 15824 1.26 - 2.51: 1296 2.51 - 3.77: 149 3.77 - 5.03: 49 5.03 - 6.29: 12 Bond angle restraints: 17330 Sorted by residual: angle pdb=" CA TYR A 970 " pdb=" CB TYR A 970 " pdb=" CG TYR A 970 " ideal model delta sigma weight residual 113.90 120.18 -6.28 1.80e+00 3.09e-01 1.22e+01 angle pdb=" N GLY A1080 " pdb=" CA GLY A1080 " pdb=" C GLY A1080 " ideal model delta sigma weight residual 114.64 109.84 4.80 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA TRP A1062 " pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 113.60 107.59 6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C CYS A 928 " pdb=" N HIS A 929 " pdb=" CA HIS A 929 " ideal model delta sigma weight residual 121.24 116.86 4.38 1.44e+00 4.82e-01 9.25e+00 angle pdb=" N ASN A1196 " pdb=" CA ASN A1196 " pdb=" C ASN A1196 " ideal model delta sigma weight residual 107.41 113.43 -6.02 2.02e+00 2.45e-01 8.87e+00 ... (remaining 17325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 4424 20.74 - 41.49: 213 41.49 - 62.23: 57 62.23 - 82.97: 24 82.97 - 103.71: 7 Dihedral angle restraints: 4725 sinusoidal: 2602 harmonic: 2123 Sorted by residual: dihedral pdb=" CB CYS A 928 " pdb=" SG CYS A 928 " pdb=" SG CYS A 946 " pdb=" CB CYS A 946 " ideal model delta sinusoidal sigma weight residual 93.00 168.88 -75.88 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CA PRO A 873 " pdb=" C PRO A 873 " pdb=" N SER A 874 " pdb=" CA SER A 874 " ideal model delta harmonic sigma weight residual 180.00 152.54 27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA PHE A 869 " pdb=" C PHE A 869 " pdb=" N PRO A 870 " pdb=" CA PRO A 870 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 565 0.054 - 0.107: 144 0.107 - 0.161: 34 0.161 - 0.214: 2 0.214 - 0.268: 4 Chirality restraints: 749 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG A3003 " pdb=" ND2 ASN A 913 " pdb=" C2 NAG A3003 " pdb=" O5 NAG A3003 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLN A 969 " pdb=" N GLN A 969 " pdb=" C GLN A 969 " pdb=" CB GLN A 969 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 746 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1197 " 0.016 2.00e-02 2.50e+03 1.92e-02 1.48e+01 pdb=" CG TRP A1197 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A1197 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A1197 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1197 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A1197 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1197 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1197 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A1197 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A1197 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A1197 " 0.041 2.00e-02 2.50e+03 pdb=" HE3 TRP A1197 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1197 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1197 " 0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP A1197 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1148 " 0.320 9.50e-02 1.11e+02 1.07e-01 1.36e+01 pdb=" NE ARG A1148 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A1148 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A1148 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1148 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A1148 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1148 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1148 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A1148 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1160 " -0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A1161 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " -0.048 5.00e-02 4.00e+02 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.02: 117 2.02 - 2.66: 13556 2.66 - 3.31: 28651 3.31 - 3.95: 35281 3.95 - 4.60: 56027 Nonbonded interactions: 133632 Sorted by model distance: nonbonded pdb=" OD2 ASP A1041 " pdb=" H ILE A1097 " model vdw 1.373 2.450 nonbonded pdb=" H THR A 948 " pdb=" OD2 ASP A 953 " model vdw 1.513 2.450 nonbonded pdb=" OE1 GLU A 707 " pdb="HE22 GLN A 782 " model vdw 1.561 2.450 nonbonded pdb=" HE1 TRP A 855 " pdb=" O ALA A1086 " model vdw 1.586 2.450 nonbonded pdb=" O GLU A 719 " pdb=" HG SER A 723 " model vdw 1.600 2.450 ... (remaining 133627 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.150 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5058 Z= 0.349 Angle : 0.961 10.815 6897 Z= 0.519 Chirality : 0.052 0.268 749 Planarity : 0.010 0.138 872 Dihedral : 14.779 103.712 2000 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.44 (0.31), residues: 583 helix: -1.08 (0.23), residues: 359 sheet: -0.64 (1.40), residues: 10 loop : -0.40 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP A1197 HIS 0.011 0.003 HIS A1089 PHE 0.021 0.004 PHE A 813 TYR 0.034 0.006 TYR A1068 ARG 0.021 0.004 ARG A1148 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 5) link_NAG-ASN : angle 5.13638 ( 15) link_ALPHA1-6 : bond 0.00736 ( 1) link_ALPHA1-6 : angle 1.50431 ( 3) link_BETA1-4 : bond 0.00728 ( 4) link_BETA1-4 : angle 3.58578 ( 12) hydrogen bonds : bond 0.20566 ( 276) hydrogen bonds : angle 8.87200 ( 789) SS BOND : bond 0.00574 ( 3) SS BOND : angle 2.97521 ( 6) covalent geometry : bond 0.00742 ( 5045) covalent geometry : angle 0.91573 ( 6861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 MET cc_start: 0.7952 (tpp) cc_final: 0.7640 (tpt) REVERT: A 914 LYS cc_start: 0.8216 (mttt) cc_final: 0.7991 (mttt) REVERT: A 961 MET cc_start: 0.9058 (mmm) cc_final: 0.8854 (mmm) REVERT: A 968 MET cc_start: 0.7227 (mtm) cc_final: 0.7006 (mtm) REVERT: A 1051 SER cc_start: 0.8965 (p) cc_final: 0.8695 (t) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3925 time to fit residues: 65.2350 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123399 restraints weight = 24976.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127683 restraints weight = 13271.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130531 restraints weight = 8188.113| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5058 Z= 0.167 Angle : 0.737 10.059 6897 Z= 0.390 Chirality : 0.043 0.212 749 Planarity : 0.008 0.117 872 Dihedral : 8.793 69.435 842 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.20 % Allowed : 2.35 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.10 (0.35), residues: 583 helix: 0.03 (0.26), residues: 358 sheet: -0.02 (1.52), residues: 10 loop : 0.04 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1062 HIS 0.011 0.002 HIS A1089 PHE 0.013 0.002 PHE A1033 TYR 0.023 0.002 TYR A 970 ARG 0.005 0.001 ARG A 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 5) link_NAG-ASN : angle 2.15577 ( 15) link_ALPHA1-6 : bond 0.00679 ( 1) link_ALPHA1-6 : angle 1.50025 ( 3) link_BETA1-4 : bond 0.00318 ( 4) link_BETA1-4 : angle 2.24211 ( 12) hydrogen bonds : bond 0.06242 ( 276) hydrogen bonds : angle 5.83146 ( 789) SS BOND : bond 0.00434 ( 3) SS BOND : angle 4.48420 ( 6) covalent geometry : bond 0.00354 ( 5045) covalent geometry : angle 0.71308 ( 6861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8505 (ttm110) REVERT: A 855 TRP cc_start: 0.8439 (m-90) cc_final: 0.8140 (m-90) REVERT: A 961 MET cc_start: 0.9046 (mmm) cc_final: 0.8812 (mmm) REVERT: A 1051 SER cc_start: 0.8859 (p) cc_final: 0.8543 (t) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.3547 time to fit residues: 48.7957 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 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 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122426 restraints weight = 25116.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126851 restraints weight = 13172.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129729 restraints weight = 8001.499| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5058 Z= 0.146 Angle : 0.638 6.518 6897 Z= 0.338 Chirality : 0.040 0.201 749 Planarity : 0.006 0.062 872 Dihedral : 6.149 33.766 842 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.35), residues: 583 helix: 0.40 (0.26), residues: 358 sheet: 0.43 (1.54), residues: 10 loop : 0.26 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1150 HIS 0.010 0.001 HIS A 832 PHE 0.019 0.002 PHE A1082 TYR 0.023 0.002 TYR A1096 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 1.67138 ( 15) link_ALPHA1-6 : bond 0.00830 ( 1) link_ALPHA1-6 : angle 1.71904 ( 3) link_BETA1-4 : bond 0.00311 ( 4) link_BETA1-4 : angle 2.10679 ( 12) hydrogen bonds : bond 0.05326 ( 276) hydrogen bonds : angle 5.39982 ( 789) SS BOND : bond 0.00932 ( 3) SS BOND : angle 3.05449 ( 6) covalent geometry : bond 0.00313 ( 5045) covalent geometry : angle 0.62166 ( 6861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 946 CYS cc_start: 0.5800 (m) cc_final: 0.5524 (m) REVERT: A 961 MET cc_start: 0.9009 (mmm) cc_final: 0.8798 (mmm) REVERT: A 1051 SER cc_start: 0.8845 (p) cc_final: 0.8524 (t) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.4241 time to fit residues: 51.4033 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123741 restraints weight = 24319.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128117 restraints weight = 12299.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130944 restraints weight = 7302.383| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 5058 Z= 0.171 Angle : 0.664 13.455 6897 Z= 0.350 Chirality : 0.041 0.233 749 Planarity : 0.005 0.053 872 Dihedral : 5.253 25.837 842 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.63 (0.35), residues: 583 helix: 0.54 (0.26), residues: 358 sheet: 0.72 (1.88), residues: 10 loop : 0.47 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 855 HIS 0.005 0.001 HIS A 963 PHE 0.018 0.002 PHE A1033 TYR 0.027 0.002 TYR A 966 ARG 0.002 0.000 ARG A 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 5) link_NAG-ASN : angle 1.46077 ( 15) link_ALPHA1-6 : bond 0.00553 ( 1) link_ALPHA1-6 : angle 1.90858 ( 3) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 2.05244 ( 12) hydrogen bonds : bond 0.04912 ( 276) hydrogen bonds : angle 5.24797 ( 789) SS BOND : bond 0.01791 ( 3) SS BOND : angle 5.45147 ( 6) covalent geometry : bond 0.00417 ( 5045) covalent geometry : angle 0.63571 ( 6861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 961 MET cc_start: 0.9012 (mmm) cc_final: 0.8807 (mmm) REVERT: A 1051 SER cc_start: 0.8870 (p) cc_final: 0.8565 (t) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3186 time to fit residues: 42.7860 Evaluate side-chains 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120167 restraints weight = 25214.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124974 restraints weight = 12361.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128130 restraints weight = 7196.849| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5058 Z= 0.147 Angle : 0.625 14.243 6897 Z= 0.329 Chirality : 0.040 0.254 749 Planarity : 0.005 0.045 872 Dihedral : 4.935 25.812 842 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.85 (0.35), residues: 583 helix: 0.79 (0.27), residues: 364 sheet: 0.95 (2.09), residues: 10 loop : 0.38 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 758 HIS 0.005 0.001 HIS A 832 PHE 0.016 0.002 PHE A1033 TYR 0.024 0.002 TYR A 970 ARG 0.002 0.000 ARG A1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 1.32310 ( 15) link_ALPHA1-6 : bond 0.00385 ( 1) link_ALPHA1-6 : angle 1.54773 ( 3) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.79422 ( 12) hydrogen bonds : bond 0.04341 ( 276) hydrogen bonds : angle 4.97833 ( 789) SS BOND : bond 0.01719 ( 3) SS BOND : angle 4.11956 ( 6) covalent geometry : bond 0.00345 ( 5045) covalent geometry : angle 0.60622 ( 6861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7401 (mtt-85) REVERT: A 961 MET cc_start: 0.8995 (mmm) cc_final: 0.8775 (mmm) REVERT: A 1051 SER cc_start: 0.9009 (p) cc_final: 0.8621 (t) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3026 time to fit residues: 38.4497 Evaluate side-chains 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122882 restraints weight = 25561.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127404 restraints weight = 12943.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130414 restraints weight = 7745.121| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 5058 Z= 0.135 Angle : 0.602 12.823 6897 Z= 0.316 Chirality : 0.039 0.231 749 Planarity : 0.005 0.072 872 Dihedral : 4.835 26.373 842 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.27 (0.36), residues: 583 helix: 1.09 (0.27), residues: 359 sheet: 0.98 (2.11), residues: 10 loop : 0.64 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 761 HIS 0.011 0.001 HIS A 832 PHE 0.013 0.002 PHE A1022 TYR 0.016 0.001 TYR A 970 ARG 0.003 0.000 ARG A1044 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 1.23561 ( 15) link_ALPHA1-6 : bond 0.00333 ( 1) link_ALPHA1-6 : angle 1.59832 ( 3) link_BETA1-4 : bond 0.00263 ( 4) link_BETA1-4 : angle 1.68283 ( 12) hydrogen bonds : bond 0.04094 ( 276) hydrogen bonds : angle 4.89670 ( 789) SS BOND : bond 0.01177 ( 3) SS BOND : angle 3.27470 ( 6) covalent geometry : bond 0.00322 ( 5045) covalent geometry : angle 0.58803 ( 6861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 ARG cc_start: 0.7256 (ttp80) cc_final: 0.7048 (ttp80) REVERT: A 942 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7482 (mtt-85) REVERT: A 961 MET cc_start: 0.8950 (mmm) cc_final: 0.8700 (mmm) REVERT: A 1051 SER cc_start: 0.8996 (p) cc_final: 0.8671 (t) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3147 time to fit residues: 38.6837 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120568 restraints weight = 25539.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125468 restraints weight = 12566.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128696 restraints weight = 7373.459| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5058 Z= 0.151 Angle : 0.597 11.213 6897 Z= 0.315 Chirality : 0.039 0.207 749 Planarity : 0.005 0.064 872 Dihedral : 4.820 26.383 842 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.37 (0.36), residues: 583 helix: 1.22 (0.27), residues: 359 sheet: 0.34 (1.96), residues: 10 loop : 0.61 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 761 HIS 0.008 0.001 HIS A 832 PHE 0.019 0.002 PHE A1036 TYR 0.016 0.002 TYR A 776 ARG 0.002 0.000 ARG A1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 5) link_NAG-ASN : angle 1.21387 ( 15) link_ALPHA1-6 : bond 0.00241 ( 1) link_ALPHA1-6 : angle 1.56162 ( 3) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 1.70544 ( 12) hydrogen bonds : bond 0.03973 ( 276) hydrogen bonds : angle 4.86522 ( 789) SS BOND : bond 0.00986 ( 3) SS BOND : angle 2.77718 ( 6) covalent geometry : bond 0.00349 ( 5045) covalent geometry : angle 0.58525 ( 6861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 ARG cc_start: 0.7103 (ttp80) cc_final: 0.6890 (ttp80) REVERT: A 961 MET cc_start: 0.8991 (mmm) cc_final: 0.8750 (mmm) REVERT: A 1051 SER cc_start: 0.8961 (p) cc_final: 0.8542 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3063 time to fit residues: 37.1254 Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121209 restraints weight = 25843.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126132 restraints weight = 12707.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129355 restraints weight = 7460.317| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5058 Z= 0.135 Angle : 0.579 10.024 6897 Z= 0.304 Chirality : 0.039 0.185 749 Planarity : 0.005 0.061 872 Dihedral : 4.747 26.781 842 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.48 (0.36), residues: 583 helix: 1.32 (0.27), residues: 360 sheet: -0.02 (1.90), residues: 10 loop : 0.65 (0.49), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 761 HIS 0.006 0.001 HIS A 832 PHE 0.015 0.001 PHE A1033 TYR 0.017 0.001 TYR A 776 ARG 0.002 0.000 ARG A1044 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 5) link_NAG-ASN : angle 1.14921 ( 15) link_ALPHA1-6 : bond 0.00287 ( 1) link_ALPHA1-6 : angle 1.61386 ( 3) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.61801 ( 12) hydrogen bonds : bond 0.03803 ( 276) hydrogen bonds : angle 4.76414 ( 789) SS BOND : bond 0.00893 ( 3) SS BOND : angle 2.50013 ( 6) covalent geometry : bond 0.00314 ( 5045) covalent geometry : angle 0.56878 ( 6861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 THR cc_start: 0.9141 (m) cc_final: 0.8924 (p) REVERT: A 811 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6954 (ttp80) REVERT: A 1051 SER cc_start: 0.8958 (p) cc_final: 0.8568 (t) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4965 time to fit residues: 62.4024 Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121367 restraints weight = 25531.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126124 restraints weight = 12530.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129288 restraints weight = 7354.113| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5058 Z= 0.129 Angle : 0.563 8.945 6897 Z= 0.294 Chirality : 0.038 0.179 749 Planarity : 0.005 0.059 872 Dihedral : 4.667 27.261 842 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.62 (0.36), residues: 583 helix: 1.46 (0.27), residues: 360 sheet: -0.31 (1.92), residues: 10 loop : 0.68 (0.49), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 761 HIS 0.006 0.001 HIS A 832 PHE 0.012 0.001 PHE A1033 TYR 0.016 0.001 TYR A1096 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 1.13890 ( 15) link_ALPHA1-6 : bond 0.00298 ( 1) link_ALPHA1-6 : angle 1.60670 ( 3) link_BETA1-4 : bond 0.00284 ( 4) link_BETA1-4 : angle 1.58203 ( 12) hydrogen bonds : bond 0.03675 ( 276) hydrogen bonds : angle 4.67831 ( 789) SS BOND : bond 0.00785 ( 3) SS BOND : angle 2.25665 ( 6) covalent geometry : bond 0.00302 ( 5045) covalent geometry : angle 0.55314 ( 6861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 THR cc_start: 0.9143 (m) cc_final: 0.8918 (p) REVERT: A 811 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6833 (ttp80) REVERT: A 1051 SER cc_start: 0.8951 (p) cc_final: 0.8484 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3562 time to fit residues: 42.1352 Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122702 restraints weight = 25886.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127658 restraints weight = 12555.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130867 restraints weight = 7293.845| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5058 Z= 0.121 Angle : 0.557 8.318 6897 Z= 0.291 Chirality : 0.038 0.176 749 Planarity : 0.005 0.059 872 Dihedral : 4.605 27.199 842 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.57 (0.36), residues: 583 helix: 1.45 (0.27), residues: 372 sheet: -0.20 (2.01), residues: 10 loop : 0.53 (0.49), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 761 HIS 0.007 0.001 HIS A1089 PHE 0.010 0.001 PHE A 985 TYR 0.016 0.001 TYR A 776 ARG 0.002 0.000 ARG A1044 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 5) link_NAG-ASN : angle 1.12082 ( 15) link_ALPHA1-6 : bond 0.00252 ( 1) link_ALPHA1-6 : angle 1.59107 ( 3) link_BETA1-4 : bond 0.00281 ( 4) link_BETA1-4 : angle 1.54318 ( 12) hydrogen bonds : bond 0.03563 ( 276) hydrogen bonds : angle 4.62215 ( 789) SS BOND : bond 0.00736 ( 3) SS BOND : angle 2.20483 ( 6) covalent geometry : bond 0.00283 ( 5045) covalent geometry : angle 0.54701 ( 6861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 THR cc_start: 0.9129 (m) cc_final: 0.8898 (p) REVERT: A 811 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6924 (ttp80) REVERT: A 1051 SER cc_start: 0.8969 (p) cc_final: 0.8571 (t) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3407 time to fit residues: 42.1607 Evaluate side-chains 81 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122123 restraints weight = 25729.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127075 restraints weight = 12540.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130323 restraints weight = 7285.068| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5058 Z= 0.127 Angle : 0.545 7.440 6897 Z= 0.284 Chirality : 0.038 0.174 749 Planarity : 0.005 0.057 872 Dihedral : 4.569 27.134 842 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.73 (0.36), residues: 583 helix: 1.60 (0.27), residues: 363 sheet: -0.19 (1.98), residues: 10 loop : 0.58 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 761 HIS 0.004 0.001 HIS A 832 PHE 0.009 0.001 PHE A 985 TYR 0.016 0.001 TYR A 776 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 5) link_NAG-ASN : angle 1.16814 ( 15) link_ALPHA1-6 : bond 0.00215 ( 1) link_ALPHA1-6 : angle 1.56319 ( 3) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 1.57573 ( 12) hydrogen bonds : bond 0.03508 ( 276) hydrogen bonds : angle 4.58630 ( 789) SS BOND : bond 0.00649 ( 3) SS BOND : angle 1.92872 ( 6) covalent geometry : bond 0.00294 ( 5045) covalent geometry : angle 0.53578 ( 6861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.42 seconds wall clock time: 71 minutes 24.62 seconds (4284.62 seconds total)