Starting phenix.real_space_refine on Thu Jul 2 14:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubc_42082/07_2026/8ubc_42082.map" } resolution = 3.29 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= 0.027 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 P 93 5.49 5 S 35 5.16 5 C 5472 2.51 5 N 1644 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9092 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2583 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 6} Chain: "I" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1849 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 41, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 72} Chain breaks: 2 Time building chain proxies: 2.16, per 1000 atoms: 0.24 Number of scatterers: 9092 At special positions: 0 Unit cell: (79, 86, 128, 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) S 35 16.00 P 93 15.00 O 1848 8.00 N 1644 7.00 C 5472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 261.2 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 77.5% alpha, 0.9% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 32 through 41 removed outlier: 3.806A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.544A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 4.026A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 4.462A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 3.643A pdb=" N LEU A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 289 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.881A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.588A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 64 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.644A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 63 removed outlier: 3.679A pdb=" N GLY C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 removed outlier: 3.524A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.711A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.644A pdb=" N MET D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.923A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.621A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 33 removed outlier: 3.529A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.512A pdb=" N GLU F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 33 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 60 removed outlier: 3.691A pdb=" N GLY F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 removed outlier: 4.196A pdb=" N LEU F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.035A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213 473 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1234 1.31 - 1.44: 3159 1.44 - 1.56: 4848 1.56 - 1.69: 183 1.69 - 1.82: 60 Bond restraints: 9484 Sorted by residual: bond pdb=" C PHE B 45 " pdb=" O PHE B 45 " ideal model delta sigma weight residual 1.235 1.185 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" CG1 ILE B 24 " pdb=" CD1 ILE B 24 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.59e+00 bond pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" CB VAL B 53 " pdb=" CG2 VAL B 53 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.55e+00 bond pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.84e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12775 2.48 - 4.96: 411 4.96 - 7.45: 60 7.45 - 9.93: 12 9.93 - 12.41: 4 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 14 " pdb=" CA THR A 14 " pdb=" CB THR A 14 " ideal model delta sigma weight residual 111.91 100.65 11.26 1.52e+00 4.33e-01 5.49e+01 angle pdb=" N LEU A 315 " pdb=" CA LEU A 315 " pdb=" C LEU A 315 " ideal model delta sigma weight residual 112.90 107.08 5.82 1.31e+00 5.83e-01 1.97e+01 angle pdb=" N LEU A 19 " pdb=" CA LEU A 19 " pdb=" C LEU A 19 " ideal model delta sigma weight residual 112.04 105.84 6.20 1.44e+00 4.82e-01 1.85e+01 angle pdb=" N TRP A 309 " pdb=" CA TRP A 309 " pdb=" C TRP A 309 " ideal model delta sigma weight residual 113.20 107.40 5.80 1.36e+00 5.41e-01 1.82e+01 angle pdb=" CA TYR C 28 " pdb=" CB TYR C 28 " pdb=" CG TYR C 28 " ideal model delta sigma weight residual 113.90 106.25 7.65 1.80e+00 3.09e-01 1.81e+01 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 5094 35.72 - 71.44: 653 71.44 - 107.16: 56 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 5808 sinusoidal: 3250 harmonic: 2558 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -79.47 -80.53 1 1.50e+01 4.44e-03 3.56e+01 dihedral pdb=" CA GLN A 322 " pdb=" C GLN A 322 " pdb=" N TYR A 323 " pdb=" CA TYR A 323 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 5805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1272 0.066 - 0.132: 239 0.132 - 0.198: 19 0.198 - 0.264: 10 0.264 - 0.330: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" P G I 4 " pdb=" OP1 G I 4 " pdb=" OP2 G I 4 " pdb=" O5' G I 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU A 200 " pdb=" CB LEU A 200 " pdb=" CD1 LEU A 200 " pdb=" CD2 LEU A 200 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 57 " pdb=" CA ILE D 57 " pdb=" CG1 ILE D 57 " pdb=" CG2 ILE D 57 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1539 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.037 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE A 231 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 29 " -0.012 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LYS A 29 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS A 29 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.030 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.010 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 520 2.70 - 3.25: 9607 3.25 - 3.80: 19821 3.80 - 4.35: 25676 4.35 - 4.90: 35984 Nonbonded interactions: 91608 Sorted by model distance: nonbonded pdb=" O SER F 62 " pdb=" OG SER F 62 " model vdw 2.145 3.040 nonbonded pdb=" O2' A I 100 " pdb=" OP2 A I 101 " model vdw 2.195 3.040 nonbonded pdb=" NH2 ARG C 36 " pdb=" OP2 U I 3 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.246 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 ... (remaining 91603 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 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 2.170 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.930 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 9484 Z= 0.336 Angle : 1.057 12.411 13262 Z= 0.612 Chirality : 0.052 0.330 1542 Planarity : 0.008 0.047 1327 Dihedral : 25.642 178.604 4158 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 37.78 Ramachandran Plot: Outliers : 4.62 % Allowed : 10.51 % Favored : 84.87 % Rotamer: Outliers : 25.31 % Allowed : 16.33 % Favored : 58.37 % 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: -5.01 (0.22), residues: 866 helix: -2.91 (0.16), residues: 617 sheet: -2.80 (1.21), residues: 12 loop : -3.94 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 127 TYR 0.035 0.004 TYR A 213 PHE 0.053 0.005 PHE A 231 TRP 0.018 0.003 TRP F 81 HIS 0.010 0.003 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.34 ( 9484) covalent geometry : angle 1.05664 / 0.61 (13262) hydrogen bonds : bond 0.23731 / 15.49 ( 545) hydrogen bonds : angle 10.17035 / 7.15 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 300 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6222 (mmtm) REVERT: A 7 ASN cc_start: 0.8883 (m-40) cc_final: 0.8539 (m-40) REVERT: A 23 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7771 (ptm-80) REVERT: A 103 LEU cc_start: 0.8395 (mt) cc_final: 0.8141 (mt) REVERT: A 113 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6244 (mttm) REVERT: A 119 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 157 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8178 (tttm) REVERT: A 240 GLU cc_start: 0.8606 (pt0) cc_final: 0.8320 (pp20) REVERT: A 241 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7441 (tmm160) REVERT: A 258 ILE cc_start: 0.8674 (mt) cc_final: 0.8180 (mt) REVERT: A 272 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 1 MET cc_start: 0.7103 (tmm) cc_final: 0.6865 (ttp) REVERT: B 9 LYS cc_start: 0.6888 (mtpt) cc_final: 0.6412 (mttt) REVERT: B 14 MET cc_start: 0.8785 (mtt) cc_final: 0.8565 (mtm) REVERT: B 47 LYS cc_start: 0.8210 (mttm) cc_final: 0.8001 (mtpp) REVERT: B 54 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: B 62 SER cc_start: 0.9116 (t) cc_final: 0.8879 (t) REVERT: B 64 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6817 (mm110) REVERT: B 108 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 14 MET cc_start: 0.7430 (tpt) cc_final: 0.7167 (mmt) REVERT: C 18 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8068 (tt0) REVERT: C 20 TYR cc_start: 0.8162 (t80) cc_final: 0.7623 (t80) REVERT: C 26 TYR cc_start: 0.8528 (t80) cc_final: 0.8219 (t80) REVERT: C 43 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: C 44 MET cc_start: 0.8607 (mtp) cc_final: 0.8365 (mtp) REVERT: C 52 GLN cc_start: 0.8391 (tp40) cc_final: 0.8034 (tp40) REVERT: C 82 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 52 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: D 92 HIS cc_start: 0.7554 (m-70) cc_final: 0.7147 (p-80) REVERT: D 108 GLU cc_start: 0.8391 (tt0) cc_final: 0.7939 (tp30) REVERT: E 50 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 103 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: E 108 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: F 15 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5344 (pt) REVERT: F 19 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7992 (tpp80) REVERT: F 25 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8445 (m) REVERT: F 52 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7405 (tm130) REVERT: F 54 GLU cc_start: 0.8226 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 83 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7937 (ttp-110) REVERT: F 85 LEU cc_start: 0.8650 (mt) cc_final: 0.8439 (mp) REVERT: F 119 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6191 (mtm180) REVERT: F 121 ASN cc_start: 0.8354 (m-40) cc_final: 0.8021 (m-40) REVERT: F 123 LYS cc_start: 0.4723 (OUTLIER) cc_final: 0.4327 (mmmt) outliers start: 186 outliers final: 46 residues processed: 396 average time/residue: 0.1341 time to fit residues: 67.6725 Evaluate side-chains 315 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 14 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.160152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131750 restraints weight = 14817.702| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.75 r_work: 0.3583 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 9484 Z= 0.271 Angle : 0.897 9.778 13262 Z= 0.485 Chirality : 0.051 0.333 1542 Planarity : 0.007 0.048 1327 Dihedral : 23.948 174.944 2604 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 1.73 % Allowed : 9.12 % Favored : 89.15 % Rotamer: Outliers : 10.88 % Allowed : 22.99 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.59 (0.24), residues: 866 helix: -1.93 (0.17), residues: 665 sheet: -2.03 (1.40), residues: 12 loop : -3.35 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.026 0.003 TYR A 213 PHE 0.058 0.004 PHE C 80 TRP 0.027 0.003 TRP A 15 HIS 0.010 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 ( 9484) covalent geometry : angle 0.89684 / 0.49 (13262) hydrogen bonds : bond 0.08678 / 5.73 ( 545) hydrogen bonds : angle 6.19536 / 4.30 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 253 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3969 (ppp) cc_final: 0.3530 (mmt) REVERT: A 20 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7853 (t0) REVERT: A 82 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7961 (pttm) REVERT: A 83 ASP cc_start: 0.8427 (m-30) cc_final: 0.8213 (m-30) REVERT: A 103 LEU cc_start: 0.8564 (mt) cc_final: 0.8298 (mt) REVERT: A 119 VAL cc_start: 0.9183 (m) cc_final: 0.8945 (p) REVERT: A 156 ASP cc_start: 0.7291 (m-30) cc_final: 0.6898 (m-30) REVERT: A 256 ARG cc_start: 0.6738 (mtt-85) cc_final: 0.6532 (ttm110) REVERT: B 1 MET cc_start: 0.6743 (tmm) cc_final: 0.6081 (ttp) REVERT: B 22 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7747 (mtm110) REVERT: C 19 ARG cc_start: 0.7534 (tpp80) cc_final: 0.6684 (tpp80) REVERT: C 42 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6994 (ttp-170) REVERT: C 67 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8526 (mmmm) REVERT: D 100 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: D 101 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.6932 (t) REVERT: E 17 VAL cc_start: 0.9034 (p) cc_final: 0.8766 (t) REVERT: E 40 VAL cc_start: 0.9217 (t) cc_final: 0.9014 (t) REVERT: E 50 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8423 (mt) REVERT: E 108 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: F 21 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: F 43 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: F 44 MET cc_start: 0.8829 (mtp) cc_final: 0.8598 (mtp) outliers start: 80 outliers final: 29 residues processed: 299 average time/residue: 0.1185 time to fit residues: 46.6114 Evaluate side-chains 256 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 89 GLN F 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.162576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135755 restraints weight = 14797.845| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.63 r_work: 0.3634 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9484 Z= 0.239 Angle : 0.790 10.821 13262 Z= 0.424 Chirality : 0.047 0.281 1542 Planarity : 0.006 0.052 1327 Dihedral : 23.163 175.858 2501 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 1.50 % Allowed : 9.24 % Favored : 89.26 % Rotamer: Outliers : 8.71 % Allowed : 24.08 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.94 (0.26), residues: 866 helix: -1.42 (0.18), residues: 665 sheet: -1.00 (1.55), residues: 12 loop : -3.39 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.024 0.003 TYR B 26 PHE 0.036 0.003 PHE C 80 TRP 0.016 0.002 TRP A 318 HIS 0.012 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 ( 9484) covalent geometry : angle 0.79003 / 0.42 (13262) hydrogen bonds : bond 0.07571 / 5.01 ( 545) hydrogen bonds : angle 5.85651 / 4.07 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: A 24 LYS cc_start: 0.8302 (mttp) cc_final: 0.8098 (mtpt) REVERT: A 42 ASP cc_start: 0.7939 (p0) cc_final: 0.7690 (p0) REVERT: A 103 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8487 (mt) REVERT: A 143 PHE cc_start: 0.7800 (m-10) cc_final: 0.7460 (m-10) REVERT: A 156 ASP cc_start: 0.7142 (m-30) cc_final: 0.6744 (m-30) REVERT: B 1 MET cc_start: 0.6583 (tmm) cc_final: 0.6099 (ttp) REVERT: B 22 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7705 (mtm110) REVERT: B 42 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7218 (ttm-80) REVERT: B 69 TYR cc_start: 0.7503 (m-80) cc_final: 0.7128 (m-80) REVERT: C 19 ARG cc_start: 0.7346 (tpp80) cc_final: 0.6441 (tpp80) REVERT: C 26 TYR cc_start: 0.8353 (t80) cc_final: 0.8069 (t80) REVERT: C 42 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7016 (ttp-170) REVERT: C 67 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8369 (mmmm) REVERT: C 98 GLN cc_start: 0.8243 (mt0) cc_final: 0.8041 (mt0) REVERT: D 100 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: E 17 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (t) REVERT: E 108 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: F 21 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: F 43 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: F 44 MET cc_start: 0.8786 (mtp) cc_final: 0.8502 (mtp) outliers start: 64 outliers final: 32 residues processed: 271 average time/residue: 0.1120 time to fit residues: 40.1862 Evaluate side-chains 259 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.158120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129687 restraints weight = 14976.302| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.78 r_work: 0.3560 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9484 Z= 0.237 Angle : 0.748 8.647 13262 Z= 0.403 Chirality : 0.045 0.250 1542 Planarity : 0.006 0.050 1327 Dihedral : 22.913 178.064 2489 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.66 % Favored : 90.42 % Rotamer: Outliers : 8.44 % Allowed : 25.44 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.45 (0.26), residues: 866 helix: -1.04 (0.18), residues: 665 sheet: -1.95 (1.38), residues: 14 loop : -3.23 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.022 0.003 TYR C 28 PHE 0.053 0.003 PHE A 287 TRP 0.011 0.002 TRP A 15 HIS 0.012 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 ( 9484) covalent geometry : angle 0.74834 / 0.40 (13262) hydrogen bonds : bond 0.07071 / 4.66 ( 545) hydrogen bonds : angle 5.63566 / 3.92 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 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: A 1 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3073 (mmt) REVERT: A 10 ASP cc_start: 0.7859 (t70) cc_final: 0.7414 (m-30) REVERT: A 20 ASP cc_start: 0.8324 (m-30) cc_final: 0.7889 (t0) REVERT: A 24 LYS cc_start: 0.8352 (mttp) cc_final: 0.8145 (mtpt) REVERT: A 42 ASP cc_start: 0.7910 (p0) cc_final: 0.7670 (p0) REVERT: A 103 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 143 PHE cc_start: 0.7787 (m-10) cc_final: 0.7298 (m-10) REVERT: A 156 ASP cc_start: 0.7215 (m-30) cc_final: 0.6803 (m-30) REVERT: A 300 LEU cc_start: 0.8504 (mm) cc_final: 0.8298 (pp) REVERT: B 6 GLU cc_start: 0.7262 (pm20) cc_final: 0.6857 (pm20) REVERT: B 22 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7549 (mtm110) REVERT: B 42 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7208 (ttm-80) REVERT: C 19 ARG cc_start: 0.7484 (tpp80) cc_final: 0.6829 (tpp80) REVERT: C 26 TYR cc_start: 0.8349 (t80) cc_final: 0.8036 (t80) REVERT: C 67 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8370 (mmmm) REVERT: C 90 LYS cc_start: 0.4676 (tptp) cc_final: 0.4130 (tttt) REVERT: C 108 GLU cc_start: 0.6977 (pt0) cc_final: 0.6772 (pt0) REVERT: D 100 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6180 (tm-30) REVERT: E 17 VAL cc_start: 0.8930 (p) cc_final: 0.8615 (t) REVERT: E 108 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: F 21 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: F 43 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: F 44 MET cc_start: 0.8782 (mtp) cc_final: 0.8475 (mtp) outliers start: 62 outliers final: 39 residues processed: 273 average time/residue: 0.1163 time to fit residues: 42.1212 Evaluate side-chains 260 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.159664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131448 restraints weight = 14848.347| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.78 r_work: 0.3580 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9484 Z= 0.209 Angle : 0.754 13.823 13262 Z= 0.405 Chirality : 0.046 0.226 1542 Planarity : 0.006 0.050 1327 Dihedral : 22.746 179.344 2480 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 29.32 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.89 % Favored : 90.30 % Rotamer: Outliers : 7.89 % Allowed : 28.16 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.19 (0.27), residues: 866 helix: -0.81 (0.19), residues: 664 sheet: -2.11 (1.34), residues: 14 loop : -3.26 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.023 0.002 TYR C 28 PHE 0.063 0.003 PHE A 287 TRP 0.009 0.001 TRP C 116 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 ( 9484) covalent geometry : angle 0.75431 / 0.40 (13262) hydrogen bonds : bond 0.06819 / 4.46 ( 545) hydrogen bonds : angle 5.55629 / 3.88 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4127 (ppp) cc_final: 0.3129 (mmt) REVERT: A 10 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: A 156 ASP cc_start: 0.7170 (m-30) cc_final: 0.6848 (m-30) REVERT: A 165 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8071 (mtp180) REVERT: A 300 LEU cc_start: 0.8512 (mm) cc_final: 0.8244 (pp) REVERT: B 6 GLU cc_start: 0.7290 (pm20) cc_final: 0.6925 (pm20) REVERT: B 22 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7427 (mtm110) REVERT: B 42 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: B 82 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7719 (mm) REVERT: B 89 GLN cc_start: 0.7159 (mt0) cc_final: 0.6947 (mt0) REVERT: C 19 ARG cc_start: 0.7537 (tpp80) cc_final: 0.6952 (tpp80) REVERT: C 26 TYR cc_start: 0.8237 (t80) cc_final: 0.7943 (t80) REVERT: C 67 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8265 (mmmm) REVERT: D 100 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: E 17 VAL cc_start: 0.8813 (p) cc_final: 0.8526 (t) REVERT: F 21 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: F 43 GLU cc_start: 0.7815 (tt0) cc_final: 0.7570 (mt-10) REVERT: F 44 MET cc_start: 0.8791 (mtp) cc_final: 0.8500 (mtp) outliers start: 58 outliers final: 31 residues processed: 255 average time/residue: 0.1201 time to fit residues: 40.6144 Evaluate side-chains 236 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 52 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** D 32 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 = 0.4117 r_free = 0.4117 target = 0.160018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131792 restraints weight = 14877.461| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.75 r_work: 0.3580 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9484 Z= 0.213 Angle : 0.746 9.244 13262 Z= 0.400 Chirality : 0.045 0.221 1542 Planarity : 0.006 0.055 1327 Dihedral : 22.497 179.715 2469 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.85 % Favored : 91.45 % Rotamer: Outliers : 7.07 % Allowed : 28.44 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.89 (0.27), residues: 866 helix: -0.58 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -3.18 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 256 TYR 0.025 0.002 TYR C 28 PHE 0.070 0.003 PHE A 287 TRP 0.008 0.002 TRP A 309 HIS 0.012 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 9484) covalent geometry : angle 0.74558 / 0.40 (13262) hydrogen bonds : bond 0.06645 / 4.36 ( 545) hydrogen bonds : angle 5.47766 / 3.83 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4136 (OUTLIER) cc_final: 0.3129 (mmt) REVERT: A 10 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: A 20 ASP cc_start: 0.8209 (m-30) cc_final: 0.7721 (t0) REVERT: A 143 PHE cc_start: 0.7655 (m-10) cc_final: 0.7310 (m-10) REVERT: A 165 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8068 (mtp180) REVERT: A 300 LEU cc_start: 0.8525 (mm) cc_final: 0.8132 (mt) REVERT: B 6 GLU cc_start: 0.7389 (pm20) cc_final: 0.7019 (pm20) REVERT: B 22 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7478 (mtm110) REVERT: B 42 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.6520 (ttm-80) REVERT: B 98 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7421 (mm-40) REVERT: B 105 LEU cc_start: 0.8246 (mp) cc_final: 0.7928 (mt) REVERT: C 19 ARG cc_start: 0.7479 (tpp80) cc_final: 0.6950 (tpp80) REVERT: D 100 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: E 14 MET cc_start: 0.7197 (mmm) cc_final: 0.6921 (mmm) REVERT: F 38 HIS cc_start: 0.8050 (m-70) cc_final: 0.7586 (m-70) REVERT: F 43 GLU cc_start: 0.7885 (tt0) cc_final: 0.7566 (mt-10) outliers start: 52 outliers final: 31 residues processed: 248 average time/residue: 0.1232 time to fit residues: 40.1254 Evaluate side-chains 235 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN A 308 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 32 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 = 0.4123 r_free = 0.4123 target = 0.160569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132455 restraints weight = 14877.456| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.76 r_work: 0.3592 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9484 Z= 0.207 Angle : 0.739 8.830 13262 Z= 0.397 Chirality : 0.045 0.246 1542 Planarity : 0.006 0.048 1327 Dihedral : 22.389 179.736 2461 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.08 % Favored : 91.22 % Rotamer: Outliers : 5.71 % Allowed : 28.44 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.87 (0.27), residues: 866 helix: -0.51 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -3.38 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.024 0.002 TYR A 213 PHE 0.036 0.003 PHE C 80 TRP 0.014 0.002 TRP D 116 HIS 0.017 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 ( 9484) covalent geometry : angle 0.73930 / 0.40 (13262) hydrogen bonds : bond 0.06528 / 4.27 ( 545) hydrogen bonds : angle 5.39556 / 3.78 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.3278 (mmt) REVERT: A 20 ASP cc_start: 0.8206 (m-30) cc_final: 0.7785 (t0) REVERT: A 143 PHE cc_start: 0.7822 (m-10) cc_final: 0.7508 (m-10) REVERT: A 156 ASP cc_start: 0.7318 (m-30) cc_final: 0.7117 (m-30) REVERT: A 300 LEU cc_start: 0.8492 (mm) cc_final: 0.8106 (mt) REVERT: B 6 GLU cc_start: 0.7398 (pm20) cc_final: 0.7104 (pm20) REVERT: B 22 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7506 (mtm110) REVERT: B 42 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.6522 (ttm-80) REVERT: B 98 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7451 (mt0) REVERT: C 19 ARG cc_start: 0.7412 (tpp80) cc_final: 0.6727 (tpp80) REVERT: C 108 GLU cc_start: 0.6657 (pt0) cc_final: 0.6220 (pt0) REVERT: D 100 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: F 43 GLU cc_start: 0.7866 (tt0) cc_final: 0.7536 (mt-10) outliers start: 42 outliers final: 29 residues processed: 236 average time/residue: 0.1104 time to fit residues: 34.6441 Evaluate side-chains 231 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.160844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132776 restraints weight = 14828.086| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.76 r_work: 0.3603 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9484 Z= 0.205 Angle : 0.730 8.825 13262 Z= 0.393 Chirality : 0.044 0.213 1542 Planarity : 0.006 0.058 1327 Dihedral : 22.319 179.778 2459 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.51 % Favored : 91.80 % Rotamer: Outliers : 5.44 % Allowed : 29.39 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.75 (0.27), residues: 866 helix: -0.44 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -3.32 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.029 0.003 TYR A 213 PHE 0.063 0.003 PHE A 287 TRP 0.010 0.001 TRP D 116 HIS 0.016 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 9484) covalent geometry : angle 0.73007 / 0.39 (13262) hydrogen bonds : bond 0.06405 / 4.20 ( 545) hydrogen bonds : angle 5.38353 / 3.78 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.3297 (mmt) REVERT: A 20 ASP cc_start: 0.8177 (m-30) cc_final: 0.7780 (t0) REVERT: A 143 PHE cc_start: 0.7649 (m-10) cc_final: 0.7378 (m-10) REVERT: A 156 ASP cc_start: 0.7138 (m-30) cc_final: 0.6864 (m-30) REVERT: B 6 GLU cc_start: 0.7412 (pm20) cc_final: 0.7095 (pm20) REVERT: B 22 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7496 (mtm110) REVERT: B 42 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.6559 (ttm-80) REVERT: B 54 GLU cc_start: 0.8342 (tp30) cc_final: 0.7593 (tt0) REVERT: B 69 TYR cc_start: 0.7236 (m-80) cc_final: 0.6855 (m-80) REVERT: B 98 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7446 (mt0) REVERT: C 19 ARG cc_start: 0.7476 (tpp80) cc_final: 0.6707 (tpp80) REVERT: C 108 GLU cc_start: 0.6704 (pt0) cc_final: 0.6133 (pt0) REVERT: D 100 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: E 14 MET cc_start: 0.7270 (mmm) cc_final: 0.6667 (mmm) REVERT: F 43 GLU cc_start: 0.7842 (tt0) cc_final: 0.7525 (mt-10) outliers start: 40 outliers final: 30 residues processed: 233 average time/residue: 0.1190 time to fit residues: 36.7780 Evaluate side-chains 229 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 121 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.160533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132329 restraints weight = 14727.118| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.79 r_work: 0.3580 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9484 Z= 0.196 Angle : 0.728 8.873 13262 Z= 0.392 Chirality : 0.043 0.225 1542 Planarity : 0.006 0.063 1327 Dihedral : 22.227 179.771 2459 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.85 % Favored : 91.45 % Rotamer: Outliers : 4.90 % Allowed : 29.66 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.68 (0.27), residues: 866 helix: -0.40 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.21 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.027 0.002 TYR C 28 PHE 0.033 0.003 PHE C 80 TRP 0.031 0.002 TRP A 318 HIS 0.009 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 9484) covalent geometry : angle 0.72796 / 0.39 (13262) hydrogen bonds : bond 0.06321 / 4.16 ( 545) hydrogen bonds : angle 5.34893 / 3.75 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4290 (OUTLIER) cc_final: 0.3234 (mmt) REVERT: A 20 ASP cc_start: 0.8154 (m-30) cc_final: 0.7714 (t0) REVERT: A 83 ASP cc_start: 0.8473 (m-30) cc_final: 0.8168 (m-30) REVERT: A 84 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7775 (mtm-85) REVERT: A 143 PHE cc_start: 0.7605 (m-10) cc_final: 0.7340 (m-10) REVERT: A 156 ASP cc_start: 0.7150 (m-30) cc_final: 0.6863 (m-30) REVERT: A 256 ARG cc_start: 0.5672 (ttm110) cc_final: 0.5347 (ttm110) REVERT: B 6 GLU cc_start: 0.7407 (pm20) cc_final: 0.7142 (pm20) REVERT: B 42 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6553 (ttm-80) REVERT: B 54 GLU cc_start: 0.8353 (tp30) cc_final: 0.7627 (tt0) REVERT: B 69 TYR cc_start: 0.7262 (m-80) cc_final: 0.6878 (m-80) REVERT: C 19 ARG cc_start: 0.7440 (tpp80) cc_final: 0.6682 (tpp80) REVERT: C 108 GLU cc_start: 0.6626 (pt0) cc_final: 0.6063 (pt0) REVERT: C 111 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6865 (mtt180) REVERT: E 14 MET cc_start: 0.7175 (mmm) cc_final: 0.6908 (mmm) REVERT: F 43 GLU cc_start: 0.7867 (tt0) cc_final: 0.7541 (mt-10) outliers start: 36 outliers final: 28 residues processed: 240 average time/residue: 0.1216 time to fit residues: 38.3324 Evaluate side-chains 231 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 10.9990 chunk 39 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.160776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132249 restraints weight = 14769.449| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.82 r_work: 0.3575 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9484 Z= 0.216 Angle : 0.757 9.979 13262 Z= 0.408 Chirality : 0.045 0.302 1542 Planarity : 0.007 0.063 1327 Dihedral : 22.143 179.291 2453 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.31 % Favored : 91.11 % Rotamer: Outliers : 4.22 % Allowed : 30.48 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.71 (0.27), residues: 866 helix: -0.43 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -3.24 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 122 TYR 0.027 0.002 TYR C 28 PHE 0.046 0.003 PHE A 287 TRP 0.011 0.002 TRP D 116 HIS 0.009 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 ( 9484) covalent geometry : angle 0.75750 / 0.41 (13262) hydrogen bonds : bond 0.06421 / 4.21 ( 545) hydrogen bonds : angle 5.36850 / 3.79 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4278 (OUTLIER) cc_final: 0.3237 (mmt) REVERT: A 20 ASP cc_start: 0.8106 (m-30) cc_final: 0.7689 (t0) REVERT: A 83 ASP cc_start: 0.8501 (m-30) cc_final: 0.8123 (m-30) REVERT: A 143 PHE cc_start: 0.7591 (m-10) cc_final: 0.7322 (m-10) REVERT: A 156 ASP cc_start: 0.7119 (m-30) cc_final: 0.6813 (m-30) REVERT: B 1 MET cc_start: 0.6504 (tpp) cc_final: 0.6082 (tpp) REVERT: B 6 GLU cc_start: 0.7463 (pm20) cc_final: 0.7146 (pm20) REVERT: B 42 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.6418 (ttm-80) REVERT: B 54 GLU cc_start: 0.8224 (tp30) cc_final: 0.7451 (tt0) REVERT: B 69 TYR cc_start: 0.7306 (m-80) cc_final: 0.6903 (m-80) REVERT: C 19 ARG cc_start: 0.7512 (tpp80) cc_final: 0.6700 (tpp80) REVERT: C 26 TYR cc_start: 0.8509 (t80) cc_final: 0.8200 (t80) REVERT: C 108 GLU cc_start: 0.6751 (pt0) cc_final: 0.6149 (pt0) REVERT: C 111 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6969 (mtt180) REVERT: E 14 MET cc_start: 0.7250 (mmm) cc_final: 0.6845 (mmm) REVERT: F 43 GLU cc_start: 0.7927 (tt0) cc_final: 0.7574 (mt-10) outliers start: 31 outliers final: 29 residues processed: 222 average time/residue: 0.1123 time to fit residues: 33.4131 Evaluate side-chains 226 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN F 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.162347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134491 restraints weight = 14785.067| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.76 r_work: 0.3620 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9484 Z= 0.213 Angle : 0.756 9.021 13262 Z= 0.408 Chirality : 0.046 0.325 1542 Planarity : 0.006 0.064 1327 Dihedral : 22.093 177.007 2453 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.66 % Favored : 90.76 % Rotamer: Outliers : 4.76 % Allowed : 30.07 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.71 (0.27), residues: 866 helix: -0.43 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -3.25 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 119 TYR 0.028 0.002 TYR C 28 PHE 0.033 0.003 PHE C 80 TRP 0.011 0.002 TRP D 116 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 9484) covalent geometry : angle 0.75617 / 0.41 (13262) hydrogen bonds : bond 0.06401 / 4.18 ( 545) hydrogen bonds : angle 5.42015 / 3.85 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.13 seconds wall clock time: 39 minutes 31.54 seconds (2371.54 seconds total)