Starting phenix.real_space_refine on Fri Jul 25 07:13:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2t_43758/07_2025/8w2t_43758_neut.cif" } resolution = 2.52 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3298 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 26 5.16 5 C 2846 2.51 5 N 816 2.21 5 O 798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4488 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2243 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2243 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1635 SG CYS D1081 55.052 15.823 63.245 1.00 73.54 S ATOM 1695 SG CYS D1089 52.081 16.456 65.323 1.00 67.99 S ATOM 1721 SG CYS D1092 54.777 18.829 65.304 1.00 66.89 S ATOM 3878 SG CYS Q1081 12.251 34.067 11.902 1.00 85.28 S ATOM 3938 SG CYS Q1089 14.760 32.502 9.703 1.00 77.24 S ATOM 3964 SG CYS Q1092 15.927 35.341 12.028 1.00 75.79 S Time building chain proxies: 3.67, per 1000 atoms: 0.82 Number of scatterers: 4488 At special positions: 0 Unit cell: (94.164, 100.772, 76.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 26 16.00 O 798 8.00 N 816 7.00 C 2846 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 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 490.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" ND1 HIS D1084 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1092 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1089 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1081 " pdb=" ZN Q1201 " pdb="ZN ZN Q1201 " - pdb=" ND1 HIS Q1084 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1089 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1081 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1092 " Number of angles added : 6 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 44.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'D' and resid 875 through 886 removed outlier: 4.365A pdb=" N THR D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 889 No H-bonds generated for 'chain 'D' and resid 887 through 889' Processing helix chain 'D' and resid 890 through 897 removed outlier: 3.539A pdb=" N ARG D 896 " --> pdb=" O ASP D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 905 Processing helix chain 'D' and resid 908 through 916 Processing helix chain 'D' and resid 919 through 935 Processing helix chain 'D' and resid 937 through 940 Processing helix chain 'D' and resid 941 through 946 Processing helix chain 'D' and resid 962 through 975 removed outlier: 3.525A pdb=" N THR D 975 " --> pdb=" O GLU D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1019 Processing helix chain 'D' and resid 1035 through 1043 removed outlier: 3.566A pdb=" N HIS D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1049 Processing helix chain 'D' and resid 1064 through 1070 removed outlier: 3.594A pdb=" N GLN D1070 " --> pdb=" O SER D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1078 Processing helix chain 'D' and resid 1143 through 1145 No H-bonds generated for 'chain 'D' and resid 1143 through 1145' Processing helix chain 'Q' and resid 876 through 885 Processing helix chain 'Q' and resid 887 through 889 No H-bonds generated for 'chain 'Q' and resid 887 through 889' Processing helix chain 'Q' and resid 890 through 897 Processing helix chain 'Q' and resid 900 through 905 Processing helix chain 'Q' and resid 908 through 915 Processing helix chain 'Q' and resid 919 through 935 Processing helix chain 'Q' and resid 937 through 940 Processing helix chain 'Q' and resid 941 through 947 removed outlier: 3.562A pdb=" N THR Q 945 " --> pdb=" O ASN Q 941 " (cutoff:3.500A) Processing helix chain 'Q' and resid 962 through 975 removed outlier: 3.609A pdb=" N THR Q 975 " --> pdb=" O GLU Q 971 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1002 through 1019 Processing helix chain 'Q' and resid 1035 through 1043 removed outlier: 3.739A pdb=" N HIS Q1041 " --> pdb=" O ASN Q1037 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1045 through 1049 Processing helix chain 'Q' and resid 1064 through 1070 removed outlier: 3.508A pdb=" N SER Q1068 " --> pdb=" O ASN Q1064 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1074 through 1078 Processing helix chain 'Q' and resid 1143 through 1145 No H-bonds generated for 'chain 'Q' and resid 1143 through 1145' Processing sheet with id=AA1, first strand: chain 'D' and resid 954 through 957 removed outlier: 5.264A pdb=" N ILE D 994 " --> pdb=" O GLN D1156 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D1156 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 996 " --> pdb=" O THR D1154 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU D1150 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA D1147 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR D1102 " --> pdb=" O ALA D1147 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG D1100 " --> pdb=" O PRO D1149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 6.253A pdb=" N PHE D1107 " --> pdb=" O THR D1126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 954 through 957 removed outlier: 6.294A pdb=" N TYR Q 992 " --> pdb=" O MET Q1158 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET Q1158 " --> pdb=" O TYR Q 992 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE Q 994 " --> pdb=" O GLN Q1156 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN Q1156 " --> pdb=" O ILE Q 994 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS Q 996 " --> pdb=" O THR Q1154 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU Q1150 " --> pdb=" O VAL Q1000 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1059 through 1062 190 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1500 1.35 - 1.47: 1121 1.47 - 1.59: 1929 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 4592 Sorted by residual: bond pdb=" CA GLY D1133 " pdb=" C GLY D1133 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.24e+00 bond pdb=" N GLY D1133 " pdb=" CA GLY D1133 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.84e+00 bond pdb=" CA ASN Q 941 " pdb=" C ASN Q 941 " ideal model delta sigma weight residual 1.532 1.524 0.008 6.50e-03 2.37e+04 1.38e+00 bond pdb=" C ASN Q 941 " pdb=" O ASN Q 941 " ideal model delta sigma weight residual 1.233 1.238 -0.005 4.80e-03 4.34e+04 1.03e+00 bond pdb=" CA ILE Q 917 " pdb=" CB ILE Q 917 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.37e-01 ... (remaining 4587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 5675 0.80 - 1.59: 418 1.59 - 2.39: 62 2.39 - 3.18: 14 3.18 - 3.98: 13 Bond angle restraints: 6182 Sorted by residual: angle pdb=" N ASN D 947 " pdb=" CA ASN D 947 " pdb=" CB ASN D 947 " ideal model delta sigma weight residual 112.78 109.70 3.08 1.53e+00 4.27e-01 4.06e+00 angle pdb=" N ILE D1051 " pdb=" CA ILE D1051 " pdb=" C ILE D1051 " ideal model delta sigma weight residual 109.34 113.32 -3.98 2.08e+00 2.31e-01 3.66e+00 angle pdb=" CA ALA Q1057 " pdb=" C ALA Q1057 " pdb=" N GLY Q1058 " ideal model delta sigma weight residual 114.60 117.08 -2.48 1.30e+00 5.92e-01 3.63e+00 angle pdb=" CA ALA Q1057 " pdb=" C ALA Q1057 " pdb=" O ALA Q1057 " ideal model delta sigma weight residual 122.63 120.45 2.18 1.29e+00 6.01e-01 2.86e+00 angle pdb=" N GLY D1133 " pdb=" CA GLY D1133 " pdb=" C GLY D1133 " ideal model delta sigma weight residual 111.67 113.22 -1.55 9.20e-01 1.18e+00 2.85e+00 ... (remaining 6177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 2407 17.74 - 35.47: 202 35.47 - 53.21: 72 53.21 - 70.95: 15 70.95 - 88.68: 8 Dihedral angle restraints: 2704 sinusoidal: 1090 harmonic: 1614 Sorted by residual: dihedral pdb=" CA PHE Q1098 " pdb=" C PHE Q1098 " pdb=" N CYS Q1099 " pdb=" CA CYS Q1099 " ideal model delta harmonic sigma weight residual -180.00 -158.82 -21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE D1098 " pdb=" C PHE D1098 " pdb=" N CYS D1099 " pdb=" CA CYS D1099 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU D1018 " pdb=" C GLU D1018 " pdb=" N GLU D1019 " pdb=" CA GLU D1019 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 361 0.027 - 0.053: 199 0.053 - 0.080: 47 0.080 - 0.107: 24 0.107 - 0.133: 17 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA VAL D1000 " pdb=" N VAL D1000 " pdb=" C VAL D1000 " pdb=" CB VAL D1000 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE Q1153 " pdb=" N ILE Q1153 " pdb=" C ILE Q1153 " pdb=" CB ILE Q1153 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE D 997 " pdb=" N ILE D 997 " pdb=" C ILE D 997 " pdb=" CB ILE D 997 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 645 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D1084 " 0.005 2.00e-02 2.50e+03 1.19e-02 2.13e+00 pdb=" CG HIS D1084 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS D1084 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS D1084 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS D1084 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS D1084 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER Q 959 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO Q 960 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO Q 960 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO Q 960 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 959 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO D 960 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 960 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 960 " -0.015 5.00e-02 4.00e+02 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 52 2.67 - 3.23: 4134 3.23 - 3.79: 6719 3.79 - 4.34: 9849 4.34 - 4.90: 15580 Nonbonded interactions: 36334 Sorted by model distance: nonbonded pdb=" O ILE Q1091 " pdb=" NE2 GLN Q1156 " model vdw 2.118 3.120 nonbonded pdb=" NH2 ARG D1027 " pdb=" OE2 GLU D1063 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR Q 900 " pdb=" OD1 ASP Q 902 " model vdw 2.193 3.040 nonbonded pdb=" OE2 GLU Q 964 " pdb=" OH TYR Q1151 " model vdw 2.212 3.040 nonbonded pdb=" OG SER D1106 " pdb=" OG1 THR D1126 " model vdw 2.323 3.040 ... (remaining 36329 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'Q' } 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 0.656 4600 Z= 0.388 Angle : 0.631 19.235 6188 Z= 0.306 Chirality : 0.039 0.133 648 Planarity : 0.003 0.027 804 Dihedral : 16.005 88.682 1684 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.65 % Allowed : 11.90 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.35), residues: 564 helix: 0.72 (0.38), residues: 204 sheet: -0.51 (0.41), residues: 132 loop : -0.08 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q1006 HIS 0.017 0.001 HIS D1084 PHE 0.015 0.001 PHE D1055 TYR 0.009 0.001 TYR D1090 ARG 0.002 0.000 ARG Q1087 Details of bonding type rmsd hydrogen bonds : bond 0.17126 ( 190) hydrogen bonds : angle 5.89281 ( 516) metal coordination : bond 0.25628 ( 8) metal coordination : angle 12.82236 ( 6) covalent geometry : bond 0.00240 ( 4592) covalent geometry : angle 0.48940 ( 6182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.503 Fit side-chains REVERT: D 963 LYS cc_start: 0.7675 (pttt) cc_final: 0.7468 (ptpp) REVERT: Q 1087 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6826 (ttm110) REVERT: Q 1113 MET cc_start: 0.7132 (ptt) cc_final: 0.6834 (pp-130) outliers start: 3 outliers final: 0 residues processed: 102 average time/residue: 1.6099 time to fit residues: 168.7898 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN D 966 GLN D1041 HIS Q 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152348 restraints weight = 4623.360| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.86 r_work: 0.3729 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 4600 Z= 0.194 Angle : 0.576 7.042 6188 Z= 0.318 Chirality : 0.045 0.150 648 Planarity : 0.004 0.042 804 Dihedral : 5.053 21.604 628 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.60 % Allowed : 13.20 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 564 helix: 0.55 (0.37), residues: 210 sheet: 0.01 (0.45), residues: 120 loop : 0.16 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP Q1006 HIS 0.007 0.002 HIS D1084 PHE 0.023 0.002 PHE D 881 TYR 0.015 0.002 TYR Q 992 ARG 0.004 0.001 ARG Q1027 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 190) hydrogen bonds : angle 4.90937 ( 516) metal coordination : bond 0.05702 ( 8) metal coordination : angle 4.71224 ( 6) covalent geometry : bond 0.00433 ( 4592) covalent geometry : angle 0.55720 ( 6182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.544 Fit side-chains REVERT: D 963 LYS cc_start: 0.7516 (pttt) cc_final: 0.7285 (pttm) REVERT: D 1138 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: Q 896 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7082 (mmt-90) REVERT: Q 1067 LYS cc_start: 0.7607 (ttmp) cc_final: 0.7162 (ttpm) REVERT: Q 1087 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6837 (ttm110) REVERT: Q 1113 MET cc_start: 0.7797 (ptt) cc_final: 0.7083 (pp-130) outliers start: 12 outliers final: 4 residues processed: 78 average time/residue: 1.3787 time to fit residues: 111.1578 Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1138 GLU Chi-restraints excluded: chain Q residue 896 ARG Chi-restraints excluded: chain Q residue 1072 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153805 restraints weight = 4673.115| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.87 r_work: 0.3746 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4600 Z= 0.130 Angle : 0.472 5.190 6188 Z= 0.263 Chirality : 0.041 0.141 648 Planarity : 0.003 0.029 804 Dihedral : 4.729 21.289 628 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.60 % Allowed : 13.85 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.36), residues: 564 helix: 0.67 (0.37), residues: 214 sheet: 0.26 (0.46), residues: 116 loop : 0.15 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1006 HIS 0.004 0.001 HIS Q 909 PHE 0.016 0.002 PHE Q 881 TYR 0.010 0.001 TYR D1142 ARG 0.003 0.000 ARG Q1027 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 190) hydrogen bonds : angle 4.51056 ( 516) metal coordination : bond 0.02315 ( 8) metal coordination : angle 2.79783 ( 6) covalent geometry : bond 0.00287 ( 4592) covalent geometry : angle 0.46391 ( 6182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.534 Fit side-chains REVERT: D 969 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: D 1138 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: Q 1067 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7493 (tttp) REVERT: Q 1087 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6883 (ttm110) outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 1.4258 time to fit residues: 107.4823 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1138 GLU Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 1072 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.178979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152249 restraints weight = 4705.811| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.83 r_work: 0.3726 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4600 Z= 0.140 Angle : 0.485 7.101 6188 Z= 0.269 Chirality : 0.042 0.138 648 Planarity : 0.003 0.030 804 Dihedral : 4.725 21.913 628 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.03 % Allowed : 14.29 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.36), residues: 564 helix: 0.65 (0.36), residues: 214 sheet: 0.23 (0.47), residues: 116 loop : 0.10 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q1006 HIS 0.004 0.001 HIS Q 909 PHE 0.016 0.002 PHE D 881 TYR 0.010 0.002 TYR Q 992 ARG 0.002 0.000 ARG Q1027 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 190) hydrogen bonds : angle 4.48813 ( 516) metal coordination : bond 0.01882 ( 8) metal coordination : angle 2.54260 ( 6) covalent geometry : bond 0.00317 ( 4592) covalent geometry : angle 0.47858 ( 6182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.499 Fit side-chains REVERT: Q 1014 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7605 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7774 (ttmp) cc_final: 0.7499 (tttp) REVERT: Q 1087 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6862 (ttm110) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 1.3636 time to fit residues: 105.7245 Evaluate side-chains 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1070 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148571 restraints weight = 4806.807| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.85 r_work: 0.3706 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4600 Z= 0.159 Angle : 0.497 6.147 6188 Z= 0.277 Chirality : 0.042 0.138 648 Planarity : 0.003 0.030 804 Dihedral : 4.778 22.378 628 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.46 % Allowed : 14.72 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 564 helix: 0.59 (0.36), residues: 214 sheet: 0.14 (0.47), residues: 116 loop : 0.03 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D1006 HIS 0.005 0.001 HIS Q1021 PHE 0.017 0.002 PHE D 881 TYR 0.011 0.002 TYR D1142 ARG 0.002 0.000 ARG D1027 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 190) hydrogen bonds : angle 4.54195 ( 516) metal coordination : bond 0.01868 ( 8) metal coordination : angle 2.52631 ( 6) covalent geometry : bond 0.00365 ( 4592) covalent geometry : angle 0.49100 ( 6182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: Q 991 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7279 (ttt180) REVERT: Q 1014 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7671 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7837 (ttmp) cc_final: 0.7516 (tttp) REVERT: Q 1087 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.6938 (ttm110) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 1.8588 time to fit residues: 152.2369 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Chi-restraints excluded: chain Q residue 1102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 922 HIS D 941 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.176326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147829 restraints weight = 4754.110| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.83 r_work: 0.3700 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4600 Z= 0.174 Angle : 0.518 6.638 6188 Z= 0.288 Chirality : 0.043 0.136 648 Planarity : 0.003 0.031 804 Dihedral : 4.842 22.919 628 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.33 % Allowed : 14.29 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.35), residues: 564 helix: 0.49 (0.36), residues: 214 sheet: 0.08 (0.46), residues: 116 loop : -0.03 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP Q1006 HIS 0.005 0.001 HIS Q1021 PHE 0.017 0.002 PHE D 881 TYR 0.012 0.002 TYR D1142 ARG 0.002 0.000 ARG Q1013 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 190) hydrogen bonds : angle 4.59026 ( 516) metal coordination : bond 0.01843 ( 8) metal coordination : angle 2.64239 ( 6) covalent geometry : bond 0.00407 ( 4592) covalent geometry : angle 0.51201 ( 6182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: Q 991 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7276 (ttt180) REVERT: Q 1014 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7681 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7601 (tttm) REVERT: Q 1087 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6901 (ttm110) outliers start: 20 outliers final: 10 residues processed: 81 average time/residue: 1.5512 time to fit residues: 130.0026 Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1140 VAL Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1067 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Chi-restraints excluded: chain Q residue 1102 THR Chi-restraints excluded: chain Q residue 1106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149445 restraints weight = 4733.312| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.83 r_work: 0.3723 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4600 Z= 0.133 Angle : 0.475 7.023 6188 Z= 0.264 Chirality : 0.041 0.138 648 Planarity : 0.003 0.030 804 Dihedral : 4.667 22.199 628 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.25 % Allowed : 15.37 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.36), residues: 564 helix: 0.57 (0.36), residues: 214 sheet: 0.06 (0.46), residues: 116 loop : 0.02 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1006 HIS 0.004 0.001 HIS Q 924 PHE 0.015 0.001 PHE Q 881 TYR 0.010 0.001 TYR D1142 ARG 0.001 0.000 ARG Q1027 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 190) hydrogen bonds : angle 4.44502 ( 516) metal coordination : bond 0.01304 ( 8) metal coordination : angle 1.84941 ( 6) covalent geometry : bond 0.00302 ( 4592) covalent geometry : angle 0.47136 ( 6182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: Q 910 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7564 (ttpp) REVERT: Q 991 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7278 (ttt180) REVERT: Q 1014 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7641 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7221 (ttpm) REVERT: Q 1087 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6925 (ttm110) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 2.2611 time to fit residues: 194.4931 Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1067 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Chi-restraints excluded: chain Q residue 1102 THR Chi-restraints excluded: chain Q residue 1106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 41 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN D1022 ASN ** Q1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149802 restraints weight = 4778.849| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.84 r_work: 0.3727 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4600 Z= 0.124 Angle : 0.475 7.781 6188 Z= 0.262 Chirality : 0.041 0.136 648 Planarity : 0.003 0.030 804 Dihedral : 4.602 21.879 628 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.25 % Allowed : 15.80 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.36), residues: 564 helix: 0.64 (0.36), residues: 214 sheet: 0.08 (0.47), residues: 116 loop : 0.04 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1006 HIS 0.004 0.001 HIS Q 924 PHE 0.013 0.001 PHE Q 881 TYR 0.017 0.002 TYR Q1071 ARG 0.002 0.000 ARG Q 883 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 190) hydrogen bonds : angle 4.40511 ( 516) metal coordination : bond 0.01193 ( 8) metal coordination : angle 1.85492 ( 6) covalent geometry : bond 0.00281 ( 4592) covalent geometry : angle 0.47201 ( 6182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: Q 991 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6964 (ttt90) REVERT: Q 1014 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7636 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7366 (tttp) REVERT: Q 1087 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.6930 (ttm110) REVERT: Q 1108 LEU cc_start: 0.8574 (mp) cc_final: 0.8144 (mp) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 1.8818 time to fit residues: 165.2615 Evaluate side-chains 82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1140 VAL Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1067 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1102 THR Chi-restraints excluded: chain Q residue 1106 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN ** Q1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.178801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152465 restraints weight = 4741.282| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.81 r_work: 0.3721 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4600 Z= 0.114 Angle : 0.479 8.045 6188 Z= 0.260 Chirality : 0.041 0.138 648 Planarity : 0.003 0.029 804 Dihedral : 4.501 21.560 628 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.16 % Allowed : 17.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.36), residues: 564 helix: 0.72 (0.36), residues: 214 sheet: 0.10 (0.47), residues: 116 loop : 0.04 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D1006 HIS 0.004 0.001 HIS Q 909 PHE 0.014 0.001 PHE Q 881 TYR 0.010 0.001 TYR D1142 ARG 0.002 0.000 ARG Q1027 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 190) hydrogen bonds : angle 4.34796 ( 516) metal coordination : bond 0.01031 ( 8) metal coordination : angle 1.57152 ( 6) covalent geometry : bond 0.00256 ( 4592) covalent geometry : angle 0.47658 ( 6182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.639 Fit side-chains REVERT: Q 910 LYS cc_start: 0.7948 (mmmt) cc_final: 0.7577 (ttpp) REVERT: Q 991 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: Q 1014 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7634 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7848 (ttmp) cc_final: 0.7244 (ttpm) REVERT: Q 1087 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.6923 (ttm110) REVERT: Q 1108 LEU cc_start: 0.8562 (mp) cc_final: 0.8123 (mp) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 2.0097 time to fit residues: 162.2263 Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Chi-restraints excluded: chain Q residue 1106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN D1022 ASN ** Q1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.177832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149493 restraints weight = 4737.164| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.82 r_work: 0.3725 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4600 Z= 0.136 Angle : 0.489 8.372 6188 Z= 0.268 Chirality : 0.041 0.136 648 Planarity : 0.003 0.029 804 Dihedral : 4.598 21.960 628 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.03 % Allowed : 16.45 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.36), residues: 564 helix: 0.66 (0.36), residues: 214 sheet: 0.10 (0.46), residues: 116 loop : 0.09 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1006 HIS 0.004 0.001 HIS Q 924 PHE 0.014 0.001 PHE Q 881 TYR 0.014 0.002 TYR Q1071 ARG 0.001 0.000 ARG Q1128 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 190) hydrogen bonds : angle 4.40556 ( 516) metal coordination : bond 0.01265 ( 8) metal coordination : angle 1.96175 ( 6) covalent geometry : bond 0.00310 ( 4592) covalent geometry : angle 0.48574 ( 6182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.665 Fit side-chains REVERT: D 932 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7386 (ttp-110) REVERT: D 969 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: Q 910 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7593 (ttpp) REVERT: Q 991 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7021 (ttt90) REVERT: Q 1014 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7694 (ttmt) REVERT: Q 1067 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7276 (ttpm) REVERT: Q 1087 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.6959 (ttm110) REVERT: Q 1108 LEU cc_start: 0.8562 (mp) cc_final: 0.8142 (mp) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 2.0884 time to fit residues: 168.9439 Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain Q residue 953 THR Chi-restraints excluded: chain Q residue 991 ARG Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1067 LYS Chi-restraints excluded: chain Q residue 1072 VAL Chi-restraints excluded: chain Q residue 1099 CYS Chi-restraints excluded: chain Q residue 1102 THR Chi-restraints excluded: chain Q residue 1106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 941 ASN ** Q1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148653 restraints weight = 4765.692| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.83 r_work: 0.3716 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4600 Z= 0.155 Angle : 0.514 8.583 6188 Z= 0.280 Chirality : 0.042 0.134 648 Planarity : 0.003 0.030 804 Dihedral : 4.665 22.236 628 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.25 % Allowed : 16.23 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.36), residues: 564 helix: 0.59 (0.36), residues: 214 sheet: 0.10 (0.47), residues: 116 loop : 0.02 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1006 HIS 0.004 0.001 HIS Q1021 PHE 0.014 0.002 PHE D 881 TYR 0.011 0.002 TYR D1142 ARG 0.002 0.000 ARG Q 883 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 190) hydrogen bonds : angle 4.46378 ( 516) metal coordination : bond 0.01403 ( 8) metal coordination : angle 2.08253 ( 6) covalent geometry : bond 0.00361 ( 4592) covalent geometry : angle 0.51063 ( 6182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.62 seconds wall clock time: 101 minutes 23.46 seconds (6083.46 seconds total)