Starting phenix.real_space_refine on Fri Oct 23 07:49:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ec_68193/10_2026/22ec_68193.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5462 2.51 5 N 1461 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8668 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2882 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 12, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2897 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2889 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 1.44, per 1000 atoms: 0.17 Number of scatterers: 8668 At special positions: 0 Unit cell: (75.492, 76.424, 220.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1712 8.00 N 1461 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.03 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.03 Simple disulfide: pdb=" SG CYS E1106 " - pdb=" SG CYS E1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " 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: 0.55 Conformation dependent library (CDL) restraints added in 244.2 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 45.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'E' and resid 805 through 811 Processing helix chain 'E' and resid 814 through 823 removed outlier: 3.767A pdb=" N GLU E 823 " --> pdb=" O GLN E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 832 Processing helix chain 'E' and resid 988 through 1106 removed outlier: 3.907A pdb=" N GLU E 992 " --> pdb=" O GLN E 988 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E1035 " --> pdb=" O GLN E1031 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN E1066 " --> pdb=" O GLU E1062 " (cutoff:3.500A) Processing helix chain 'E' and resid 1230 through 1236 Processing helix chain 'E' and resid 1263 through 1277 Processing helix chain 'E' and resid 1278 through 1281 removed outlier: 4.108A pdb=" N ILE E1281 " --> pdb=" O GLU E1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1278 through 1281' Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 821 Processing helix chain 'B' and resid 822 through 825 removed outlier: 3.644A pdb=" N GLY B 825 " --> pdb=" O ARG B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 826 through 832 removed outlier: 3.840A pdb=" N LYS B 830 " --> pdb=" O GLN B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1107 removed outlier: 3.506A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 994 " --> pdb=" O LEU B 990 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 995 " --> pdb=" O SER B 991 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B1003 " --> pdb=" O ASN B 999 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B1077 " --> pdb=" O GLY B1073 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B1107 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1236 Processing helix chain 'B' and resid 1262 through 1278 Processing helix chain 'C' and resid 805 through 810 Processing helix chain 'C' and resid 814 through 821 Processing helix chain 'C' and resid 822 through 825 removed outlier: 3.714A pdb=" N GLY C 825 " --> pdb=" O ARG C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 822 through 825' Processing helix chain 'C' and resid 826 through 832 removed outlier: 3.553A pdb=" N LYS C 830 " --> pdb=" O GLN C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1106 removed outlier: 3.586A pdb=" N ASP C1059 " --> pdb=" O ILE C1055 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C1060 " --> pdb=" O GLN C1056 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C1061 " --> pdb=" O ARG C1057 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C1069 " --> pdb=" O ALA C1065 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1236 Processing helix chain 'C' and resid 1262 through 1278 removed outlier: 3.785A pdb=" N GLU C1278 " --> pdb=" O LYS C1274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 779 through 780 Processing sheet with id=AA2, first strand: chain 'E' and resid 787 through 788 Processing sheet with id=AA3, first strand: chain 'E' and resid 792 through 795 Processing sheet with id=AA4, first strand: chain 'E' and resid 1212 through 1213 removed outlier: 7.134A pdb=" N GLN E1212 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N TYR C 794 " --> pdb=" O GLN E1212 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C1134 " --> pdb=" O ILE C 795 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.971A pdb=" N LYS B 779 " --> pdb=" O SER B1151 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER B1151 " --> pdb=" O LYS B 779 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 791 through 796 removed outlier: 3.576A pdb=" N VAL B1128 " --> pdb=" O TYR B1135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AA8, first strand: chain 'C' and resid 1164 through 1165 431 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.70 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: 2888 1.35 - 1.46: 1973 1.46 - 1.58: 3918 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 8821 Sorted by residual: bond pdb=" C SER B1279 " pdb=" O SER B1279 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.30e-02 5.92e+03 1.13e+00 bond pdb=" C ALA B1193 " pdb=" N PRO B1194 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.37e-01 bond pdb=" C ALA E1193 " pdb=" N PRO E1194 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.31e-01 bond pdb=" C PRO C1220 " pdb=" N PRO C1221 " ideal model delta sigma weight residual 1.332 1.342 -0.011 1.32e-02 5.74e+03 6.51e-01 bond pdb=" C PRO E1220 " pdb=" N PRO E1221 " ideal model delta sigma weight residual 1.331 1.341 -0.010 1.31e-02 5.83e+03 6.16e-01 ... (remaining 8816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11871 1.79 - 3.59: 93 3.59 - 5.38: 14 5.38 - 7.18: 1 7.18 - 8.97: 1 Bond angle restraints: 11980 Sorted by residual: angle pdb=" N ILE B1123 " pdb=" CA ILE B1123 " pdb=" C ILE B1123 " ideal model delta sigma weight residual 111.62 109.39 2.23 7.90e-01 1.60e+00 8.00e+00 angle pdb=" N ILE E1123 " pdb=" CA ILE E1123 " pdb=" C ILE E1123 " ideal model delta sigma weight residual 111.62 109.45 2.17 7.90e-01 1.60e+00 7.52e+00 angle pdb=" N SER B1279 " pdb=" CA SER B1279 " pdb=" C SER B1279 " ideal model delta sigma weight residual 112.13 108.47 3.66 1.37e+00 5.33e-01 7.14e+00 angle pdb=" CA LEU C1155 " pdb=" CB LEU C1155 " pdb=" CG LEU C1155 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" N TYR B1280 " pdb=" CA TYR B1280 " pdb=" C TYR B1280 " ideal model delta sigma weight residual 107.73 111.57 -3.84 1.61e+00 3.86e-01 5.70e+00 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5056 17.21 - 34.43: 226 34.43 - 51.64: 36 51.64 - 68.86: 0 68.86 - 86.07: 2 Dihedral angle restraints: 5320 sinusoidal: 2059 harmonic: 3261 Sorted by residual: dihedral pdb=" CA PRO E1220 " pdb=" C PRO E1220 " pdb=" N PRO E1221 " pdb=" CA PRO E1221 " ideal model delta harmonic sigma weight residual -180.00 -164.64 -15.36 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" N LEU E 990 " pdb=" CA LEU E 990 " pdb=" CB LEU E 990 " pdb=" CG LEU E 990 " ideal model delta sinusoidal sigma weight residual -180.00 -128.61 -51.39 3 1.50e+01 4.44e-03 9.01e+00 dihedral pdb=" CB GLU C1183 " pdb=" CG GLU C1183 " pdb=" CD GLU C1183 " pdb=" OE1 GLU C1183 " ideal model delta sinusoidal sigma weight residual 0.00 -79.96 79.96 1 3.00e+01 1.11e-03 8.81e+00 ... (remaining 5317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 878 0.027 - 0.053: 331 0.053 - 0.080: 106 0.080 - 0.106: 52 0.106 - 0.133: 16 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CG LEU C1155 " pdb=" CB LEU C1155 " pdb=" CD1 LEU C1155 " pdb=" CD2 LEU C1155 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE B1281 " pdb=" N ILE B1281 " pdb=" C ILE B1281 " pdb=" CB ILE B1281 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA VAL C1124 " pdb=" N VAL C1124 " pdb=" C VAL C1124 " pdb=" CB VAL C1124 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1380 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B1130 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO B1131 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1131 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1131 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1130 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO C1131 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C1131 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1131 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E1130 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO E1131 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E1131 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E1131 " -0.029 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1129 2.76 - 3.29: 8993 3.29 - 3.83: 14335 3.83 - 4.36: 15603 4.36 - 4.90: 26901 Nonbonded interactions: 66961 Sorted by model distance: nonbonded pdb=" OG1 THR C 791 " pdb=" O MET C1137 " model vdw 2.221 3.040 nonbonded pdb=" O ASN B1169 " pdb=" OG SER B1189 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C1187 " pdb=" O PRO C1196 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG E1088 " pdb=" O PRO B1219 " model vdw 2.281 3.120 nonbonded pdb=" O ASN E1169 " pdb=" OG SER E1189 " model vdw 2.317 3.040 ... (remaining 66956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 775 through 843 or resid 987 through 1288)) selection = (chain 'C' and (resid 775 through 843 or resid 987 through 1288)) selection = chain 'E' } 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: 1.980 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.037 8830 Z= 0.085 Angle : 0.424 8.973 11998 Z= 0.233 Chirality : 0.036 0.133 1383 Planarity : 0.004 0.054 1572 Dihedral : 9.406 86.069 3187 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.85 % Allowed : 7.64 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.25), residues: 1104 helix: 1.35 (0.23), residues: 485 sheet: -3.15 (0.57), residues: 53 loop : -3.93 (0.21), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1088 TYR 0.008 0.001 TYR E1142 PHE 0.004 0.000 PHE B 788 TRP 0.005 0.001 TRP C1184 HIS 0.001 0.000 HIS C1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.09 ( 8821) covalent geometry : angle 0.42405 / 0.23 (11980) SS BOND : bond 0.00045 / 0.03 ( 9) SS BOND : angle 0.62301 / 0.35 ( 18) hydrogen bonds : bond 0.11784 / 7.08 ( 431) hydrogen bonds : angle 4.05958 / 2.91 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1191 PHE cc_start: 0.7528 (t80) cc_final: 0.7245 (t80) REVERT: B 780 LEU cc_start: 0.8035 (mt) cc_final: 0.7757 (pp) REVERT: B 826 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8316 (pp30) REVERT: C 782 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7354 (mm) outliers start: 47 outliers final: 8 residues processed: 151 average time/residue: 0.0904 time to fit residues: 19.3642 Evaluate side-chains 56 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 808 GLN E 832 ASN E 833 GLN E1009 GLN E1020 HIS E1023 GLN E1097 GLN E1119 GLN E1177 ASN E1254 GLN E1288 ASN B 785 ASN ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B 833 GLN B 993 ASN B 994 GLN B1002 ASN B1023 GLN B1031 GLN B1097 GLN B1119 GLN B1201 ASN B1212 GLN B1254 GLN B1271 GLN B1277 ASN C 826 GLN C 994 GLN C1016 ASN C1023 GLN C1097 GLN C1160 ASN ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.066395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051920 restraints weight = 51747.363| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 6.14 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8830 Z= 0.131 Angle : 0.565 14.606 11998 Z= 0.285 Chirality : 0.040 0.172 1383 Planarity : 0.004 0.048 1572 Dihedral : 4.851 84.209 1195 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.27 % Allowed : 12.18 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.27), residues: 1104 helix: 2.46 (0.24), residues: 485 sheet: -3.55 (0.44), residues: 85 loop : -3.40 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 822 TYR 0.029 0.001 TYR E1192 PHE 0.017 0.001 PHE B 778 TRP 0.009 0.001 TRP C1184 HIS 0.004 0.001 HIS E1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8821) covalent geometry : angle 0.56472 / 0.28 (11980) SS BOND : bond 0.00155 / 0.10 ( 9) SS BOND : angle 0.75120 / 0.40 ( 18) hydrogen bonds : bond 0.03349 / 2.08 ( 431) hydrogen bonds : angle 3.44311 / 2.43 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1191 PHE cc_start: 0.7387 (t80) cc_final: 0.6807 (t80) REVERT: E 1248 ASN cc_start: 0.8752 (p0) cc_final: 0.8533 (p0) REVERT: B 1266 MET cc_start: 0.8952 (mtt) cc_final: 0.8686 (mpp) outliers start: 22 outliers final: 15 residues processed: 73 average time/residue: 0.0701 time to fit residues: 8.0436 Evaluate side-chains 51 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 1150 VAL Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [16, 37, 11, 7, 42, 6, 83, 8, 67, 14, 92] chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 785 ASN ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.064202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049665 restraints weight = 51059.706| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 5.98 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8830 Z= 0.139 Angle : 0.576 14.188 11998 Z= 0.284 Chirality : 0.039 0.140 1383 Planarity : 0.004 0.046 1572 Dihedral : 5.032 83.356 1192 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.79 % Allowed : 12.28 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 1104 helix: 2.69 (0.24), residues: 486 sheet: -3.22 (0.47), residues: 85 loop : -3.24 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1074 TYR 0.046 0.001 TYR E1192 PHE 0.016 0.001 PHE E1191 TRP 0.004 0.001 TRP C1184 HIS 0.002 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8821) covalent geometry : angle 0.57618 / 0.28 (11980) SS BOND : bond 0.00303 / 0.19 ( 9) SS BOND : angle 0.70443 / 0.37 ( 18) hydrogen bonds : bond 0.03363 / 2.12 ( 431) hydrogen bonds : angle 3.24639 / 2.28 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1248 ASN cc_start: 0.8843 (p0) cc_final: 0.8633 (p0) REVERT: B 1171 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7333 (p90) outliers start: 27 outliers final: 21 residues processed: 72 average time/residue: 0.0770 time to fit residues: 8.5106 Evaluate side-chains 61 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1165 ILE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain E residue 1267 LEU Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 1150 VAL Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [92, 84, 72, 6, 16, 37, 96, 79, 61, 94, 1] chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 808 GLN ** C1208 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.063816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.049218 restraints weight = 52197.213| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 5.97 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8830 Z= 0.114 Angle : 0.533 10.957 11998 Z= 0.262 Chirality : 0.039 0.160 1383 Planarity : 0.004 0.047 1572 Dihedral : 5.036 84.322 1192 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.20 % Allowed : 12.69 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 1104 helix: 2.84 (0.24), residues: 486 sheet: -3.13 (0.51), residues: 73 loop : -3.10 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 822 TYR 0.013 0.001 TYR C1141 PHE 0.019 0.001 PHE E 814 TRP 0.004 0.001 TRP C1184 HIS 0.004 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8821) covalent geometry : angle 0.53276 / 0.26 (11980) SS BOND : bond 0.00198 / 0.12 ( 9) SS BOND : angle 0.75869 / 0.40 ( 18) hydrogen bonds : bond 0.03267 / 2.07 ( 431) hydrogen bonds : angle 3.20755 / 2.23 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 36 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1191 PHE cc_start: 0.7946 (t80) cc_final: 0.7348 (t80) REVERT: E 1248 ASN cc_start: 0.8889 (p0) cc_final: 0.8671 (p0) REVERT: B 1171 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7457 (p90) REVERT: C 782 ILE cc_start: 0.8046 (pt) cc_final: 0.7430 (mm) REVERT: C 1005 LEU cc_start: 0.9274 (tt) cc_final: 0.8927 (pp) outliers start: 31 outliers final: 22 residues processed: 65 average time/residue: 0.0604 time to fit residues: 6.1779 Evaluate side-chains 57 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 1150 VAL Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [15, 42, 75, 6, 106, 79, 21, 35, 68, 66, 1] chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 785 ASN ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1079 ASN B1079 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN C1176 ASN ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.060961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.046345 restraints weight = 52172.035| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 5.83 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8830 Z= 0.180 Angle : 0.621 14.642 11998 Z= 0.308 Chirality : 0.040 0.158 1383 Planarity : 0.004 0.042 1572 Dihedral : 5.488 82.091 1192 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.79 % Allowed : 14.14 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 1104 helix: 2.86 (0.24), residues: 488 sheet: -2.64 (0.51), residues: 85 loop : -3.10 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1074 TYR 0.035 0.002 TYR E1192 PHE 0.020 0.002 PHE E1191 TRP 0.003 0.001 TRP B1184 HIS 0.004 0.001 HIS E 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 8821) covalent geometry : angle 0.62063 / 0.31 (11980) SS BOND : bond 0.00447 / 0.27 ( 9) SS BOND : angle 0.93610 / 0.57 ( 18) hydrogen bonds : bond 0.03565 / 2.28 ( 431) hydrogen bonds : angle 3.33593 / 2.34 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 999 ASN cc_start: 0.9505 (m110) cc_final: 0.9289 (m-40) REVERT: B 1171 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7487 (p90) REVERT: C 782 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7650 (mm) outliers start: 27 outliers final: 18 residues processed: 59 average time/residue: 0.0665 time to fit residues: 6.1285 Evaluate side-chains 51 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1150 VAL Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [93, 91, 1, 60, 67, 54, 79, 57, 29, 27, 90] chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 785 ASN ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN ** C1208 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.059944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.045322 restraints weight = 52368.385| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 5.80 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8830 Z= 0.199 Angle : 0.622 12.805 11998 Z= 0.312 Chirality : 0.040 0.150 1383 Planarity : 0.004 0.045 1572 Dihedral : 5.614 82.776 1191 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.10 % Allowed : 14.34 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 1104 helix: 2.90 (0.24), residues: 487 sheet: -2.02 (0.59), residues: 70 loop : -3.11 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1088 TYR 0.017 0.001 TYR E1142 PHE 0.016 0.001 PHE C 778 TRP 0.004 0.001 TRP C1184 HIS 0.003 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 8821) covalent geometry : angle 0.62147 / 0.31 (11980) SS BOND : bond 0.00502 / 0.31 ( 9) SS BOND : angle 0.80012 / 0.49 ( 18) hydrogen bonds : bond 0.03600 / 2.31 ( 431) hydrogen bonds : angle 3.43252 / 2.40 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 785 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8222 (p0) REVERT: E 1191 PHE cc_start: 0.8343 (t80) cc_final: 0.8052 (t80) REVERT: E 1192 TYR cc_start: 0.7527 (m-10) cc_final: 0.7094 (m-10) REVERT: B 778 PHE cc_start: 0.8418 (m-10) cc_final: 0.8158 (m-10) REVERT: B 999 ASN cc_start: 0.9528 (m110) cc_final: 0.9307 (m-40) REVERT: B 1171 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7486 (p90) REVERT: C 782 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7806 (mm) outliers start: 30 outliers final: 18 residues processed: 60 average time/residue: 0.0733 time to fit residues: 6.9409 Evaluate side-chains 53 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [13, 50, 88, 23, 41, 11, 1, 35, 37, 25, 18] chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 785 ASN ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1208 GLN C1079 ASN ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.060273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.045731 restraints weight = 52156.753| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 5.79 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.129 Angle : 0.604 12.074 11998 Z= 0.297 Chirality : 0.040 0.174 1383 Planarity : 0.004 0.050 1572 Dihedral : 5.502 84.142 1191 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.68 % Allowed : 14.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 1104 helix: 2.90 (0.24), residues: 488 sheet: -1.79 (0.62), residues: 72 loop : -3.05 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1088 TYR 0.036 0.001 TYR B 777 PHE 0.013 0.001 PHE E 786 TRP 0.005 0.001 TRP C1184 HIS 0.003 0.001 HIS C1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8821) covalent geometry : angle 0.60368 / 0.30 (11980) SS BOND : bond 0.00305 / 0.19 ( 9) SS BOND : angle 0.81940 / 0.49 ( 18) hydrogen bonds : bond 0.03520 / 2.25 ( 431) hydrogen bonds : angle 3.44661 / 2.38 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1005 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9121 (pp) REVERT: E 1191 PHE cc_start: 0.8270 (t80) cc_final: 0.7772 (t80) REVERT: E 1192 TYR cc_start: 0.7473 (m-10) cc_final: 0.7019 (m-10) REVERT: B 999 ASN cc_start: 0.9530 (m110) cc_final: 0.9313 (m-40) REVERT: B 1171 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7120 (p90) REVERT: C 782 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7864 (mm) outliers start: 26 outliers final: 18 residues processed: 58 average time/residue: 0.0740 time to fit residues: 6.4686 Evaluate side-chains 51 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1165 ILE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [39, 54, 96, 6, 87, 40, 59, 0, 90, 5, 94] chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.059953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.045380 restraints weight = 52011.435| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.80 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8830 Z= 0.146 Angle : 0.638 15.689 11998 Z= 0.312 Chirality : 0.040 0.205 1383 Planarity : 0.004 0.055 1572 Dihedral : 5.527 84.047 1191 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.79 % Allowed : 14.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 1104 helix: 2.87 (0.24), residues: 490 sheet: -1.59 (0.63), residues: 72 loop : -3.03 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 822 TYR 0.035 0.002 TYR C1192 PHE 0.011 0.001 PHE E 786 TRP 0.004 0.001 TRP C1184 HIS 0.002 0.001 HIS C1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 8821) covalent geometry : angle 0.63792 / 0.31 (11980) SS BOND : bond 0.00332 / 0.21 ( 9) SS BOND : angle 0.80375 / 0.49 ( 18) hydrogen bonds : bond 0.03554 / 2.27 ( 431) hydrogen bonds : angle 3.54236 / 2.44 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1191 PHE cc_start: 0.8408 (t80) cc_final: 0.7668 (t80) REVERT: E 1192 TYR cc_start: 0.7535 (m-10) cc_final: 0.6950 (m-10) REVERT: B 999 ASN cc_start: 0.9518 (m110) cc_final: 0.9302 (m-40) REVERT: B 1171 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7113 (p90) REVERT: C 782 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7824 (mm) outliers start: 27 outliers final: 20 residues processed: 55 average time/residue: 0.0758 time to fit residues: 6.4807 Evaluate side-chains 52 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 30 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1165 ILE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain E residue 1210 THR Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [104, 94, 105, 93, 33, 102, 31, 78, 38, 74, 6] chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 ASN C1122 HIS ** C1208 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.059819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.045290 restraints weight = 52364.937| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 5.79 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8830 Z= 0.141 Angle : 0.634 13.558 11998 Z= 0.314 Chirality : 0.040 0.189 1383 Planarity : 0.004 0.059 1572 Dihedral : 5.543 84.655 1191 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.37 % Allowed : 15.07 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 1104 helix: 2.87 (0.24), residues: 491 sheet: -2.03 (0.56), residues: 87 loop : -2.94 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 822 TYR 0.026 0.001 TYR B 777 PHE 0.015 0.001 PHE C1136 TRP 0.006 0.001 TRP C1184 HIS 0.002 0.001 HIS B 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8821) covalent geometry : angle 0.63295 / 0.31 (11980) SS BOND : bond 0.00261 / 0.16 ( 9) SS BOND : angle 0.94593 / 0.58 ( 18) hydrogen bonds : bond 0.03575 / 2.29 ( 431) hydrogen bonds : angle 3.54606 / 2.43 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1005 LEU cc_start: 0.9427 (tt) cc_final: 0.9186 (pp) REVERT: B 999 ASN cc_start: 0.9520 (m110) cc_final: 0.9311 (m-40) REVERT: B 1171 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7120 (p90) REVERT: C 782 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7886 (mm) outliers start: 23 outliers final: 18 residues processed: 50 average time/residue: 0.0774 time to fit residues: 6.0609 Evaluate side-chains 47 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 27 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1165 ILE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain E residue 1210 THR Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [78, 15, 76, 88, 24, 92, 47, 2, 106, 35, 91] chunk 78 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.068336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.054165 restraints weight = 60661.625| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 6.04 r_work: 0.3235 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8830 Z= 0.123 Angle : 0.634 13.528 11998 Z= 0.318 Chirality : 0.040 0.283 1383 Planarity : 0.004 0.061 1572 Dihedral : 5.519 85.219 1191 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.48 % Allowed : 15.58 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 1104 helix: 2.80 (0.24), residues: 492 sheet: -2.03 (0.56), residues: 87 loop : -2.92 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 822 TYR 0.052 0.002 TYR C1192 PHE 0.027 0.001 PHE E1191 TRP 0.034 0.003 TRP C1184 HIS 0.002 0.001 HIS C1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8821) covalent geometry : angle 0.63371 / 0.32 (11980) SS BOND : bond 0.00219 / 0.14 ( 9) SS BOND : angle 0.85962 / 0.52 ( 18) hydrogen bonds : bond 0.03545 / 2.27 ( 431) hydrogen bonds : angle 3.57512 / 2.43 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 28 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1005 LEU cc_start: 0.9465 (tt) cc_final: 0.9258 (pp) REVERT: E 1191 PHE cc_start: 0.8727 (t80) cc_final: 0.8110 (t80) REVERT: E 1192 TYR cc_start: 0.7932 (m-10) cc_final: 0.7517 (m-10) REVERT: B 1171 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7272 (p90) REVERT: C 782 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8082 (mm) outliers start: 24 outliers final: 21 residues processed: 48 average time/residue: 0.0654 time to fit residues: 5.0592 Evaluate side-chains 48 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1123 ILE Chi-restraints excluded: chain E residue 1141 TYR Chi-restraints excluded: chain E residue 1162 THR Chi-restraints excluded: chain E residue 1165 ILE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1172 PHE Chi-restraints excluded: chain E residue 1210 THR Chi-restraints excluded: chain B residue 826 GLN Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1171 TYR Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [83, 9, 48, 57, 96, 85, 4, 79, 27, 23, 25] chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 ASN B1119 GLN B1277 ASN C1122 HIS ** C1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.045563 restraints weight = 52152.686| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 5.75 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.126 Angle : 0.626 13.139 11998 Z= 0.315 Chirality : 0.040 0.255 1383 Planarity : 0.004 0.061 1572 Dihedral : 5.475 84.784 1191 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.68 % Allowed : 15.58 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.28), residues: 1104 helix: 2.82 (0.24), residues: 492 sheet: -1.91 (0.56), residues: 87 loop : -2.92 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 822 TYR 0.020 0.001 TYR B 777 PHE 0.024 0.001 PHE E1191 TRP 0.027 0.002 TRP C1184 HIS 0.002 0.001 HIS C1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8821) covalent geometry : angle 0.62529 / 0.32 (11980) SS BOND : bond 0.00189 / 0.12 ( 9) SS BOND : angle 0.87482 / 0.53 ( 18) hydrogen bonds : bond 0.03523 / 2.25 ( 431) hydrogen bonds : angle 3.58588 / 2.44 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.65 seconds wall clock time: 30 minutes 6.01 seconds (1806.01 seconds total)