Starting phenix.real_space_refine on Sun Apr 27 08:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtv_18654/04_2025/8qtv_18654.cif" } resolution = 3.25 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= 0.012 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 66 5.16 5 C 3162 2.51 5 N 854 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5054 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2526 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.57, per 1000 atoms: 0.90 Number of scatterers: 5054 At special positions: 0 Unit cell: (64.6275, 114.606, 74.9679, 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) Ca 2 19.99 S 66 16.00 O 970 8.00 N 854 7.00 C 3162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.03 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS B1174 " distance=2.03 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.03 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 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: 1.38 Conformation dependent library (CDL) restraints added in 651.3 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 8 sheets defined 23.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1097 through 1102 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.691A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1150 removed outlier: 3.598A pdb=" N CYS A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A1150 " --> pdb=" O CYS A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1057 through 1064 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1096 Processing helix chain 'B' and resid 1097 through 1102 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1103 through 1108 removed outlier: 3.690A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1150 removed outlier: 3.598A pdb=" N CYS B1134 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B1150 " --> pdb=" O CYS B1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 4.333A pdb=" N ALA A 901 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1024 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A1014 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 998 " --> pdb=" O TYR A1001 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.515A pdb=" N ILE A 964 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU A 949 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 964 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 947 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 966 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A 945 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE A 944 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 930 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 948 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR A 928 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN A 950 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU A 926 " --> pdb=" O ASN A 950 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A1033 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1179 removed outlier: 3.829A pdb=" N GLY A1205 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1217 Processing sheet with id=AA5, first strand: chain 'B' and resid 918 through 920 removed outlier: 4.333A pdb=" N ALA B 901 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B1024 " --> pdb=" O ALA B 901 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B1014 " --> pdb=" O LEU B1002 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 998 " --> pdb=" O TYR B1001 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.515A pdb=" N ILE B 964 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 949 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 964 " --> pdb=" O VAL B 947 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 947 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 966 " --> pdb=" O ARG B 945 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG B 945 " --> pdb=" O ILE B 966 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE B 944 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 930 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B 948 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR B 928 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN B 950 " --> pdb=" O GLU B 926 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU B 926 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B1033 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1176 through 1179 removed outlier: 3.828A pdb=" N GLY B1205 " --> pdb=" O GLN B1179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1216 through 1217 164 hydrogen bonds defined for protein. 444 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: 1.36 Time building geometry restraints manager: 1.65 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: 1680 1.35 - 1.46: 1224 1.46 - 1.58: 2210 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 5184 Sorted by residual: bond pdb=" N VAL B1183 " pdb=" CA VAL B1183 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.75e-01 bond pdb=" CA GLU A1219 " pdb=" CB GLU A1219 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.28e-01 bond pdb=" CA GLU B1219 " pdb=" CB GLU B1219 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.05e-01 bond pdb=" N VAL A1183 " pdb=" CA VAL A1183 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.61e-01 bond pdb=" CB PRO B1077 " pdb=" CG PRO B1077 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 3.98e-01 ... (remaining 5179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 6948 1.45 - 2.90: 86 2.90 - 4.35: 18 4.35 - 5.80: 0 5.80 - 7.25: 4 Bond angle restraints: 7056 Sorted by residual: angle pdb=" C ASP B1218 " pdb=" N GLU B1219 " pdb=" CA GLU B1219 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ASP A1218 " pdb=" N GLU A1219 " pdb=" CA GLU A1219 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N ILE B 983 " pdb=" CA ILE B 983 " pdb=" C ILE B 983 " ideal model delta sigma weight residual 111.48 109.22 2.26 9.40e-01 1.13e+00 5.80e+00 angle pdb=" CA GLY B 954 " pdb=" C GLY B 954 " pdb=" N THR B 955 " ideal model delta sigma weight residual 114.85 116.83 -1.98 9.50e-01 1.11e+00 4.35e+00 angle pdb=" CA GLY A 954 " pdb=" C GLY A 954 " pdb=" N THR A 955 " ideal model delta sigma weight residual 114.85 116.83 -1.98 9.50e-01 1.11e+00 4.33e+00 ... (remaining 7051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2810 17.40 - 34.79: 255 34.79 - 52.19: 78 52.19 - 69.58: 4 69.58 - 86.98: 6 Dihedral angle restraints: 3153 sinusoidal: 1255 harmonic: 1898 Sorted by residual: dihedral pdb=" CB CYS A 953 " pdb=" SG CYS A 953 " pdb=" SG CYS A 960 " pdb=" CB CYS A 960 " ideal model delta sinusoidal sigma weight residual -86.00 -172.98 86.98 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS B 953 " pdb=" SG CYS B 953 " pdb=" SG CYS B 960 " pdb=" CB CYS B 960 " ideal model delta sinusoidal sigma weight residual -86.00 -172.94 86.94 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1189 " pdb=" SG CYS A1189 " pdb=" SG CYS A1228 " pdb=" CB CYS A1228 " ideal model delta sinusoidal sigma weight residual -86.00 -155.77 69.77 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 3150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 417 0.024 - 0.048: 192 0.048 - 0.072: 67 0.072 - 0.096: 45 0.096 - 0.120: 39 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ILE A 964 " pdb=" N ILE A 964 " pdb=" C ILE A 964 " pdb=" CB ILE A 964 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL A 905 " pdb=" N VAL A 905 " pdb=" C VAL A 905 " pdb=" CB VAL A 905 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A1020 " pdb=" N ILE A1020 " pdb=" C ILE A1020 " pdb=" CB ILE A1020 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 ... (remaining 757 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B1191 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.52e-01 pdb=" N PRO B1192 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO B1192 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B1192 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1191 " -0.013 5.00e-02 4.00e+02 1.99e-02 6.36e-01 pdb=" N PRO A1192 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A1192 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A1192 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 991 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.89e-01 pdb=" N PRO B 992 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 992 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 992 " 0.011 5.00e-02 4.00e+02 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1585 2.82 - 3.34: 4393 3.34 - 3.86: 8145 3.86 - 4.38: 8746 4.38 - 4.90: 15250 Nonbonded interactions: 38119 Sorted by model distance: nonbonded pdb=" OD2 ASP B1079 " pdb=" OG1 THR B1082 " model vdw 2.297 3.040 nonbonded pdb=" OD2 ASP A1079 " pdb=" OG1 THR A1082 " model vdw 2.298 3.040 nonbonded pdb=" O THR A1049 " pdb=" OG1 THR A1049 " model vdw 2.329 3.040 nonbonded pdb=" O THR B1049 " pdb=" OG1 THR B1049 " model vdw 2.329 3.040 nonbonded pdb=" OD2 ASP B1015 " pdb=" OG SER B1019 " model vdw 2.378 3.040 ... (remaining 38114 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.680 Find NCS groups from input model: 0.100 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.002 0.032 5213 Z= 0.074 Angle : 0.428 7.252 7114 Z= 0.216 Chirality : 0.041 0.120 760 Planarity : 0.002 0.020 934 Dihedral : 13.649 73.393 1854 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % 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: -0.99 (0.32), residues: 658 helix: 0.82 (0.45), residues: 128 sheet: 0.22 (0.52), residues: 100 loop : -1.42 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A1090 HIS 0.001 0.000 HIS B1147 PHE 0.003 0.000 PHE A1135 TYR 0.004 0.000 TYR A 906 ARG 0.001 0.000 ARG B 996 Details of bonding type rmsd hydrogen bonds : bond 0.22170 ( 164) hydrogen bonds : angle 6.10120 ( 444) SS BOND : bond 0.00131 ( 29) SS BOND : angle 0.37900 ( 58) covalent geometry : bond 0.00166 ( 5184) covalent geometry : angle 0.42841 ( 7056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2470 time to fit residues: 11.8483 Evaluate side-chains 27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 chunk 51 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.4796 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.071563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.050951 restraints weight = 14546.469| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.88 r_work: 0.2595 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5213 Z= 0.145 Angle : 0.516 6.422 7114 Z= 0.266 Chirality : 0.043 0.125 760 Planarity : 0.003 0.021 934 Dihedral : 3.269 21.439 712 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.43 % Allowed : 15.54 % Favored : 83.04 % 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: -0.46 (0.33), residues: 658 helix: 1.54 (0.47), residues: 116 sheet: 0.32 (0.48), residues: 120 loop : -1.08 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1014 HIS 0.002 0.000 HIS B1147 PHE 0.005 0.001 PHE B1028 TYR 0.006 0.001 TYR A1167 ARG 0.008 0.000 ARG B1050 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 164) hydrogen bonds : angle 4.22647 ( 444) SS BOND : bond 0.00251 ( 29) SS BOND : angle 0.71481 ( 58) covalent geometry : bond 0.00333 ( 5184) covalent geometry : angle 0.51374 ( 7056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 931 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 942 ASP cc_start: 0.8702 (t0) cc_final: 0.8335 (t0) REVERT: B 931 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6979 (tm-30) REVERT: B 942 ASP cc_start: 0.8625 (t0) cc_final: 0.8404 (t0) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.1633 time to fit residues: 7.5207 Evaluate side-chains 26 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.071025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.050039 restraints weight = 14655.830| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 5.04 r_work: 0.2522 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5213 Z= 0.156 Angle : 0.511 5.215 7114 Z= 0.265 Chirality : 0.043 0.131 760 Planarity : 0.003 0.022 934 Dihedral : 3.541 21.258 712 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.32 % Allowed : 16.96 % Favored : 80.71 % 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: -0.43 (0.33), residues: 658 helix: 1.83 (0.46), residues: 116 sheet: 0.14 (0.48), residues: 126 loop : -1.10 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1014 HIS 0.002 0.000 HIS A 910 PHE 0.005 0.001 PHE A1164 TYR 0.008 0.001 TYR A 993 ARG 0.003 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 164) hydrogen bonds : angle 4.06361 ( 444) SS BOND : bond 0.00289 ( 29) SS BOND : angle 0.75157 ( 58) covalent geometry : bond 0.00356 ( 5184) covalent geometry : angle 0.50861 ( 7056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 942 ASP cc_start: 0.8729 (t0) cc_final: 0.8359 (t0) REVERT: B 931 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 942 ASP cc_start: 0.8696 (t0) cc_final: 0.8395 (t0) outliers start: 13 outliers final: 6 residues processed: 37 average time/residue: 0.1829 time to fit residues: 9.8017 Evaluate side-chains 29 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1181 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049401 restraints weight = 14945.044| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 5.06 r_work: 0.2530 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5213 Z= 0.167 Angle : 0.528 6.608 7114 Z= 0.269 Chirality : 0.043 0.126 760 Planarity : 0.003 0.024 934 Dihedral : 3.647 21.014 712 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.68 % Allowed : 16.43 % Favored : 80.89 % 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: -0.31 (0.34), residues: 658 helix: 1.92 (0.46), residues: 116 sheet: 0.17 (0.48), residues: 124 loop : -0.98 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1014 HIS 0.002 0.001 HIS B1147 PHE 0.005 0.001 PHE B 967 TYR 0.007 0.001 TYR B1167 ARG 0.002 0.000 ARG B1050 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 164) hydrogen bonds : angle 3.95417 ( 444) SS BOND : bond 0.00292 ( 29) SS BOND : angle 0.76190 ( 58) covalent geometry : bond 0.00378 ( 5184) covalent geometry : angle 0.52537 ( 7056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 942 ASP cc_start: 0.8819 (t0) cc_final: 0.8565 (t0) REVERT: B 931 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 942 ASP cc_start: 0.8706 (t0) cc_final: 0.8438 (t0) outliers start: 15 outliers final: 12 residues processed: 40 average time/residue: 0.2198 time to fit residues: 12.8961 Evaluate side-chains 35 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.070261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.049242 restraints weight = 14716.835| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 5.03 r_work: 0.2495 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5213 Z= 0.182 Angle : 0.625 11.533 7114 Z= 0.319 Chirality : 0.045 0.200 760 Planarity : 0.003 0.025 934 Dihedral : 4.025 19.970 712 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.75 % Allowed : 16.79 % Favored : 79.46 % 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 (0.34), residues: 658 helix: 1.90 (0.45), residues: 116 sheet: 0.08 (0.48), residues: 124 loop : -0.90 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A1090 HIS 0.002 0.000 HIS B 910 PHE 0.005 0.001 PHE B1217 TYR 0.007 0.001 TYR A1167 ARG 0.004 0.000 ARG B1190 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 164) hydrogen bonds : angle 4.00190 ( 444) SS BOND : bond 0.00289 ( 29) SS BOND : angle 1.93067 ( 58) covalent geometry : bond 0.00414 ( 5184) covalent geometry : angle 0.60309 ( 7056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 942 ASP cc_start: 0.8824 (t0) cc_final: 0.8551 (t0) REVERT: B 931 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 942 ASP cc_start: 0.8770 (t0) cc_final: 0.8450 (t0) outliers start: 21 outliers final: 14 residues processed: 47 average time/residue: 0.2521 time to fit residues: 16.2328 Evaluate side-chains 37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.070316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049058 restraints weight = 14578.491| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.98 r_work: 0.2538 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5213 Z= 0.168 Angle : 0.562 5.857 7114 Z= 0.290 Chirality : 0.045 0.165 760 Planarity : 0.003 0.025 934 Dihedral : 4.115 20.591 712 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.50 % Allowed : 18.39 % Favored : 79.11 % 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 (0.34), residues: 658 helix: 1.90 (0.45), residues: 116 sheet: 0.06 (0.48), residues: 124 loop : -0.89 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A1090 HIS 0.002 0.000 HIS A 910 PHE 0.004 0.001 PHE B1217 TYR 0.007 0.001 TYR A 993 ARG 0.002 0.000 ARG B1050 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 164) hydrogen bonds : angle 4.06634 ( 444) SS BOND : bond 0.00276 ( 29) SS BOND : angle 1.12146 ( 58) covalent geometry : bond 0.00387 ( 5184) covalent geometry : angle 0.55477 ( 7056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 942 ASP cc_start: 0.8851 (t0) cc_final: 0.8565 (t0) REVERT: B 931 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B 942 ASP cc_start: 0.8746 (t0) cc_final: 0.8406 (t0) outliers start: 14 outliers final: 14 residues processed: 39 average time/residue: 0.1857 time to fit residues: 10.3469 Evaluate side-chains 37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.047252 restraints weight = 14901.716| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 4.91 r_work: 0.2507 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.006 0.038 5213 Z= 0.287 Angle : 0.631 5.369 7114 Z= 0.332 Chirality : 0.046 0.154 760 Planarity : 0.003 0.024 934 Dihedral : 4.478 19.423 712 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.04 % Allowed : 17.50 % Favored : 79.46 % 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: -0.32 (0.34), residues: 658 helix: 1.77 (0.45), residues: 116 sheet: 0.10 (0.48), residues: 120 loop : -0.91 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A1065 HIS 0.003 0.001 HIS B 910 PHE 0.009 0.001 PHE B1217 TYR 0.010 0.001 TYR A1167 ARG 0.002 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 164) hydrogen bonds : angle 4.29058 ( 444) SS BOND : bond 0.00397 ( 29) SS BOND : angle 1.18795 ( 58) covalent geometry : bond 0.00643 ( 5184) covalent geometry : angle 0.62461 ( 7056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASP cc_start: 0.8836 (t0) cc_final: 0.8494 (t0) REVERT: B 942 ASP cc_start: 0.8781 (t0) cc_final: 0.8455 (t0) outliers start: 17 outliers final: 14 residues processed: 39 average time/residue: 0.1264 time to fit residues: 7.1853 Evaluate side-chains 38 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 ILE Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.070859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.048942 restraints weight = 15019.289| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 5.25 r_work: 0.2533 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5213 Z= 0.139 Angle : 0.569 5.550 7114 Z= 0.294 Chirality : 0.044 0.159 760 Planarity : 0.003 0.026 934 Dihedral : 4.142 18.488 712 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.68 % Allowed : 18.93 % Favored : 78.39 % 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: -0.35 (0.34), residues: 658 helix: 1.94 (0.45), residues: 116 sheet: -0.10 (0.48), residues: 124 loop : -0.93 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A1090 HIS 0.001 0.000 HIS B1147 PHE 0.005 0.001 PHE B1217 TYR 0.007 0.001 TYR B 993 ARG 0.002 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 164) hydrogen bonds : angle 4.09265 ( 444) SS BOND : bond 0.00241 ( 29) SS BOND : angle 0.82817 ( 58) covalent geometry : bond 0.00328 ( 5184) covalent geometry : angle 0.56627 ( 7056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASP cc_start: 0.8843 (t0) cc_final: 0.8508 (t0) REVERT: B 942 ASP cc_start: 0.8749 (t0) cc_final: 0.8403 (t0) outliers start: 15 outliers final: 15 residues processed: 41 average time/residue: 0.2627 time to fit residues: 14.3834 Evaluate side-chains 40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.073209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.051754 restraints weight = 14298.199| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 5.09 r_work: 0.2564 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5213 Z= 0.094 Angle : 0.548 5.913 7114 Z= 0.280 Chirality : 0.044 0.157 760 Planarity : 0.003 0.028 934 Dihedral : 3.740 18.739 712 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.25 % Allowed : 20.00 % Favored : 78.75 % 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: -0.24 (0.33), residues: 658 helix: 2.09 (0.45), residues: 114 sheet: 0.55 (0.52), residues: 100 loop : -1.00 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1090 HIS 0.001 0.000 HIS B1147 PHE 0.005 0.001 PHE B 944 TYR 0.005 0.001 TYR A 993 ARG 0.002 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.02512 ( 164) hydrogen bonds : angle 3.77627 ( 444) SS BOND : bond 0.00176 ( 29) SS BOND : angle 0.58100 ( 58) covalent geometry : bond 0.00234 ( 5184) covalent geometry : angle 0.54758 ( 7056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASP cc_start: 0.8815 (t0) cc_final: 0.8401 (t0) REVERT: B 942 ASP cc_start: 0.8726 (t0) cc_final: 0.8338 (t0) REVERT: B 1201 ARG cc_start: 0.9037 (ptp-170) cc_final: 0.8353 (mtt90) outliers start: 7 outliers final: 7 residues processed: 35 average time/residue: 0.2834 time to fit residues: 12.8660 Evaluate side-chains 34 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.072992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.051599 restraints weight = 14329.754| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.98 r_work: 0.2555 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5213 Z= 0.104 Angle : 0.586 9.052 7114 Z= 0.293 Chirality : 0.044 0.160 760 Planarity : 0.003 0.028 934 Dihedral : 3.738 22.245 712 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.79 % Allowed : 20.36 % Favored : 77.86 % 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: -0.22 (0.33), residues: 658 helix: 2.09 (0.45), residues: 114 sheet: 0.61 (0.51), residues: 100 loop : -0.99 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1090 HIS 0.002 0.000 HIS B1147 PHE 0.004 0.001 PHE B 944 TYR 0.004 0.001 TYR A1167 ARG 0.002 0.000 ARG B1050 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 164) hydrogen bonds : angle 3.76678 ( 444) SS BOND : bond 0.00196 ( 29) SS BOND : angle 0.63509 ( 58) covalent geometry : bond 0.00255 ( 5184) covalent geometry : angle 0.58567 ( 7056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASP cc_start: 0.8809 (t0) cc_final: 0.8404 (t0) REVERT: B 942 ASP cc_start: 0.8740 (t0) cc_final: 0.8352 (t0) outliers start: 10 outliers final: 10 residues processed: 39 average time/residue: 0.2070 time to fit residues: 10.5950 Evaluate side-chains 39 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1181 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.072393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.050779 restraints weight = 14661.674| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 5.12 r_work: 0.2541 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5213 Z= 0.113 Angle : 0.576 7.827 7114 Z= 0.290 Chirality : 0.044 0.153 760 Planarity : 0.003 0.028 934 Dihedral : 3.793 22.864 712 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.79 % Allowed : 20.00 % Favored : 78.21 % 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: -0.21 (0.33), residues: 658 helix: 1.98 (0.46), residues: 116 sheet: 0.65 (0.51), residues: 100 loop : -0.98 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1090 HIS 0.002 0.000 HIS A1147 PHE 0.011 0.001 PHE A1028 TYR 0.005 0.001 TYR A1167 ARG 0.002 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 164) hydrogen bonds : angle 3.79358 ( 444) SS BOND : bond 0.00207 ( 29) SS BOND : angle 0.67087 ( 58) covalent geometry : bond 0.00272 ( 5184) covalent geometry : angle 0.57533 ( 7056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.39 seconds wall clock time: 52 minutes 1.55 seconds (3121.55 seconds total)