Starting phenix.real_space_refine on Wed Aug 5 07:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubc_42082/08_2026/8ubc_42082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubc_42082/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2026/8ubc_42082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2026/8ubc_42082.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2026/8ubc_42082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2026/8ubc_42082.cif" } 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-2.2rc3-6140/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: 1.84, per 1000 atoms: 0.20 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: 0.62 Conformation dependent library (CDL) restraints added in 154.8 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: 1.29 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: 1.26 Time building geometry restraints manager: 0.78 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: 12714 2.48 - 4.96: 471 4.96 - 7.45: 61 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=" O5' U I 7 " pdb=" C5' U I 7 " pdb=" C4' U I 7 " ideal model delta sigma weight residual 109.40 113.64 -4.24 8.00e-01 1.56e+00 2.81e+01 angle pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " ideal model delta sigma weight residual 108.20 112.32 -4.12 8.00e-01 1.56e+00 2.66e+01 angle pdb=" C3' C I 20 " pdb=" O3' C I 20 " pdb=" P G I 21 " ideal model delta sigma weight residual 119.70 125.21 -5.51 1.20e+00 6.94e-01 2.11e+01 angle pdb=" O5' C I 107 " pdb=" C5' C I 107 " pdb=" C4' C I 107 " ideal model delta sigma weight residual 109.40 113.06 -3.66 8.00e-01 1.56e+00 2.10e+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: 1187 0.066 - 0.132: 288 0.132 - 0.198: 56 0.198 - 0.264: 9 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- 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= 0.344 Angle : 1.099 12.411 13262 Z= 0.668 Chirality : 0.060 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 0.00738 / 0.34 ( 9484) covalent geometry : angle 1.09881 / 0.67 (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 : 0.321 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: 0.6223 (mmtm) REVERT: A 7 ASN cc_start: 0.8883 (m-40) cc_final: 0.8609 (m-40) REVERT: A 23 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7772 (ptm-80) REVERT: A 103 LEU cc_start: 0.8395 (mt) cc_final: 0.8142 (mt) REVERT: A 113 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6245 (mttm) REVERT: A 119 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8732 (p) 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: 0.7439 (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: 0.8000 (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: 0.7975 (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: 0.7464 (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: 48 residues processed: 396 average time/residue: 0.1179 time to fit residues: 59.7609 Evaluate side-chains 316 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 208 ARG 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 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 = 0.4115 r_free = 0.4115 target = 0.159843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131438 restraints weight = 14806.656| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.74 r_work: 0.3573 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9484 Z= 0.270 Angle : 0.900 9.743 13262 Z= 0.477 Chirality : 0.053 0.335 1542 Planarity : 0.007 0.058 1327 Dihedral : 23.802 174.744 2608 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 33.64 Ramachandran Plot: Outliers : 1.73 % Allowed : 9.12 % Favored : 89.15 % Rotamer: Outliers : 11.16 % Allowed : 22.86 % Favored : 65.99 % 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: -3.51 (0.25), residues: 866 helix: -1.88 (0.17), residues: 665 sheet: -2.16 (1.37), residues: 12 loop : -3.27 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.026 0.003 TYR C 28 PHE 0.061 0.004 PHE C 80 TRP 0.023 0.003 TRP A 15 HIS 0.009 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 ( 9484) covalent geometry : angle 0.90015 / 0.48 (13262) hydrogen bonds : bond 0.08766 / 5.78 ( 545) hydrogen bonds : angle 6.20114 / 4.31 ( 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 329 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4009 (ppp) cc_final: 0.3508 (mmt) REVERT: A 20 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7814 (t0) REVERT: A 82 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7967 (pttm) REVERT: A 83 ASP cc_start: 0.8460 (m-30) cc_final: 0.8220 (m-30) REVERT: A 103 LEU cc_start: 0.8597 (mt) cc_final: 0.8328 (mt) REVERT: A 119 VAL cc_start: 0.9193 (m) cc_final: 0.8952 (p) REVERT: B 1 MET cc_start: 0.6772 (tmm) cc_final: 0.6059 (ttp) REVERT: B 22 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7641 (mtm110) REVERT: C 30 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8555 (mm) REVERT: C 42 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6991 (ttp-170) REVERT: C 67 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8528 (mmmm) REVERT: C 90 LYS cc_start: 0.4145 (tttt) cc_final: 0.3797 (tptp) REVERT: D 100 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: D 101 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.6986 (t) REVERT: E 17 VAL cc_start: 0.9049 (p) cc_final: 0.8769 (t) REVERT: E 40 VAL cc_start: 0.9223 (t) cc_final: 0.9011 (t) REVERT: E 94 MET cc_start: 0.8256 (mtp) cc_final: 0.8034 (mtm) REVERT: F 21 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: F 43 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: F 44 MET cc_start: 0.8836 (mtp) cc_final: 0.8635 (mtp) outliers start: 82 outliers final: 28 residues processed: 296 average time/residue: 0.1207 time to fit residues: 47.2050 Evaluate side-chains 253 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 208 ARG 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 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 30 ILE 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 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: 0.7980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 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 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.163400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136694 restraints weight = 14794.208| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.60 r_work: 0.3638 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9484 Z= 0.232 Angle : 0.793 10.937 13262 Z= 0.424 Chirality : 0.047 0.289 1542 Planarity : 0.007 0.057 1327 Dihedral : 22.943 175.736 2494 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 1.50 % Allowed : 9.12 % Favored : 89.38 % Rotamer: Outliers : 8.71 % Allowed : 23.54 % Favored : 67.76 % 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: -2.95 (0.26), residues: 866 helix: -1.44 (0.18), residues: 664 sheet: -1.05 (1.54), residues: 12 loop : -3.29 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.025 0.003 TYR B 26 PHE 0.035 0.003 PHE C 80 TRP 0.016 0.002 TRP A 318 HIS 0.007 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 ( 9484) covalent geometry : angle 0.79333 / 0.42 (13262) hydrogen bonds : bond 0.07603 / 5.03 ( 545) hydrogen bonds : angle 5.87678 / 4.09 ( 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 300 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 42 ASP cc_start: 0.7945 (p0) cc_final: 0.7687 (p0) REVERT: A 103 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 143 PHE cc_start: 0.7785 (m-10) cc_final: 0.7416 (m-10) REVERT: A 156 ASP cc_start: 0.7097 (m-30) cc_final: 0.6725 (m-30) REVERT: B 1 MET cc_start: 0.6592 (tmm) cc_final: 0.6108 (ttp) REVERT: B 22 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7595 (mtm110) REVERT: B 42 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7249 (ttm-80) REVERT: B 54 GLU cc_start: 0.8277 (tp30) cc_final: 0.8062 (tp30) REVERT: B 69 TYR cc_start: 0.7552 (m-80) cc_final: 0.7165 (m-80) REVERT: C 19 ARG cc_start: 0.7287 (tpp80) cc_final: 0.6353 (tpp80) REVERT: C 26 TYR cc_start: 0.8370 (t80) cc_final: 0.8168 (t80) REVERT: C 30 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8439 (mm) REVERT: C 42 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7022 (ttp-170) REVERT: C 67 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8369 (mmmm) REVERT: C 90 LYS cc_start: 0.3851 (tttt) cc_final: 0.3637 (tptp) REVERT: D 100 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6198 (tm-30) REVERT: E 17 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8709 (t) REVERT: F 21 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: F 43 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: F 44 MET cc_start: 0.8785 (mtp) cc_final: 0.8558 (mtp) REVERT: F 54 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 64 outliers final: 32 residues processed: 278 average time/residue: 0.1015 time to fit residues: 37.6468 Evaluate side-chains 260 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 208 ARG 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 30 ILE 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 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 16 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 62 SER 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: 0.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 0.0060 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 B 64 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.159090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131113 restraints weight = 14891.911| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.73 r_work: 0.3575 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9484 Z= 0.220 Angle : 0.755 8.692 13262 Z= 0.406 Chirality : 0.046 0.250 1542 Planarity : 0.006 0.060 1327 Dihedral : 22.694 176.335 2484 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.31 % Favored : 90.76 % Rotamer: Outliers : 8.16 % Allowed : 25.71 % 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: -2.40 (0.26), residues: 866 helix: -1.01 (0.18), residues: 663 sheet: -1.05 (1.50), residues: 12 loop : -3.23 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 256 TYR 0.021 0.003 TYR C 28 PHE 0.056 0.003 PHE A 287 TRP 0.013 0.002 TRP C 116 HIS 0.015 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 ( 9484) covalent geometry : angle 0.75529 / 0.41 (13262) hydrogen bonds : bond 0.07083 / 4.66 ( 545) hydrogen bonds : angle 5.63374 / 3.94 ( 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 288 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3151 (mmt) REVERT: A 10 ASP cc_start: 0.7804 (t70) cc_final: 0.7482 (m-30) REVERT: A 20 ASP cc_start: 0.8338 (m-30) cc_final: 0.7934 (t0) REVERT: A 42 ASP cc_start: 0.7898 (p0) cc_final: 0.7653 (p0) REVERT: A 103 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 143 PHE cc_start: 0.7735 (m-10) cc_final: 0.7064 (m-10) REVERT: A 156 ASP cc_start: 0.7271 (m-30) cc_final: 0.6885 (m-30) REVERT: A 256 ARG cc_start: 0.6126 (mtp-110) cc_final: 0.5870 (ttm-80) REVERT: A 300 LEU cc_start: 0.8282 (mm) cc_final: 0.8080 (mt) REVERT: B 42 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7258 (ttm-80) REVERT: B 54 GLU cc_start: 0.8414 (tp30) cc_final: 0.8211 (tp30) REVERT: B 69 TYR cc_start: 0.7430 (m-80) cc_final: 0.6999 (m-80) REVERT: C 19 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7138 (tpp80) REVERT: C 22 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6946 (mtm110) REVERT: C 26 TYR cc_start: 0.8328 (t80) cc_final: 0.8059 (t80) REVERT: C 30 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8222 (mm) REVERT: C 67 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8362 (mmmm) REVERT: C 90 LYS cc_start: 0.3844 (tttt) cc_final: 0.3528 (tptp) REVERT: D 47 LYS cc_start: 0.7988 (mttp) cc_final: 0.7781 (mttp) REVERT: D 100 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6255 (tm-30) REVERT: E 89 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.6147 (mt0) REVERT: F 21 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: F 43 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: F 44 MET cc_start: 0.8751 (mtp) cc_final: 0.8477 (mtp) outliers start: 60 outliers final: 38 residues processed: 270 average time/residue: 0.1051 time to fit residues: 37.4940 Evaluate side-chains 248 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG 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 30 ILE 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 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 88 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 THR 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: 0.7980 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 80 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 ** C 92 HIS ** 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4120 r_free = 0.4120 target = 0.160369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132622 restraints weight = 14798.763| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.72 r_work: 0.3601 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9484 Z= 0.199 Angle : 0.756 14.057 13262 Z= 0.402 Chirality : 0.046 0.270 1542 Planarity : 0.006 0.053 1327 Dihedral : 22.513 178.508 2483 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 28.33 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.55 % Favored : 90.76 % Rotamer: Outliers : 7.07 % Allowed : 27.48 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.27), residues: 866 helix: -0.79 (0.19), residues: 663 sheet: -1.11 (1.50), residues: 12 loop : -3.22 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.019 0.002 TYR C 28 PHE 0.063 0.003 PHE A 287 TRP 0.009 0.002 TRP A 15 HIS 0.010 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 9484) covalent geometry : angle 0.75595 / 0.40 (13262) hydrogen bonds : bond 0.06832 / 4.44 ( 545) hydrogen bonds : angle 5.49052 / 3.83 ( 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 267 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4157 (ppp) cc_final: 0.3122 (mmt) REVERT: A 107 TYR cc_start: 0.8298 (m-80) cc_final: 0.7685 (m-80) REVERT: A 113 LYS cc_start: 0.7332 (mttt) cc_final: 0.7110 (mttt) REVERT: A 156 ASP cc_start: 0.7068 (m-30) cc_final: 0.6746 (m-30) REVERT: A 165 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8068 (mtp180) REVERT: A 300 LEU cc_start: 0.8505 (mm) cc_final: 0.8248 (pp) REVERT: B 22 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7373 (mtm110) REVERT: B 42 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.6551 (ttm-80) REVERT: B 54 GLU cc_start: 0.8406 (tp30) cc_final: 0.8067 (tp30) REVERT: B 82 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7654 (mm) REVERT: C 19 ARG cc_start: 0.7461 (tpp80) cc_final: 0.6913 (tpp80) REVERT: C 22 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6871 (mtm110) REVERT: C 26 TYR cc_start: 0.8234 (t80) cc_final: 0.7847 (t80) REVERT: C 67 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8246 (mmmm) REVERT: C 90 LYS cc_start: 0.3652 (tttt) cc_final: 0.3423 (tptp) REVERT: C 108 GLU cc_start: 0.6839 (pt0) cc_final: 0.6438 (pt0) REVERT: D 100 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: E 17 VAL cc_start: 0.8935 (p) cc_final: 0.8672 (t) REVERT: E 108 GLU cc_start: 0.7464 (tp30) cc_final: 0.7128 (tp30) REVERT: F 38 HIS cc_start: 0.8080 (m-70) cc_final: 0.7713 (m-70) REVERT: F 43 GLU cc_start: 0.7827 (tt0) cc_final: 0.7554 (mt-10) REVERT: F 44 MET cc_start: 0.8729 (mtp) cc_final: 0.8485 (mtp) outliers start: 52 outliers final: 31 residues processed: 250 average time/residue: 0.1079 time to fit residues: 35.7960 Evaluate side-chains 228 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 208 ARG 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 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 82 LEU Chi-restraints excluded: chain B residue 95 THR 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 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 52 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 87 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 308 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 103 GLN C 13 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132363 restraints weight = 14876.062| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.74 r_work: 0.3601 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9484 Z= 0.199 Angle : 0.734 9.481 13262 Z= 0.392 Chirality : 0.045 0.228 1542 Planarity : 0.006 0.058 1327 Dihedral : 22.374 178.496 2471 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.62 % Favored : 91.69 % Rotamer: Outliers : 6.94 % Allowed : 28.16 % Favored : 64.90 % 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: -1.92 (0.27), residues: 866 helix: -0.60 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.18 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 19 TYR 0.023 0.002 TYR C 28 PHE 0.070 0.003 PHE A 287 TRP 0.008 0.001 TRP A 309 HIS 0.006 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 9484) covalent geometry : angle 0.73360 / 0.39 (13262) hydrogen bonds : bond 0.06636 / 4.34 ( 545) hydrogen bonds : angle 5.43399 / 3.80 ( 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 263 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4130 (OUTLIER) cc_final: 0.3091 (mmt) REVERT: A 20 ASP cc_start: 0.8183 (m-30) cc_final: 0.7695 (t0) REVERT: A 128 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6244 (ttm-80) REVERT: A 143 PHE cc_start: 0.7724 (m-10) cc_final: 0.7373 (m-10) REVERT: A 156 ASP cc_start: 0.7129 (m-30) cc_final: 0.6766 (m-30) REVERT: A 165 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8087 (mtp180) REVERT: A 300 LEU cc_start: 0.8481 (mm) cc_final: 0.8113 (mt) REVERT: B 22 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7368 (mtm110) REVERT: B 42 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.6478 (ttm-80) REVERT: B 82 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7763 (mm) REVERT: B 98 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7418 (mt0) REVERT: C 19 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7070 (tpp80) REVERT: C 22 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6897 (mtm110) REVERT: C 26 TYR cc_start: 0.8274 (t80) cc_final: 0.7754 (t80) REVERT: C 90 LYS cc_start: 0.3661 (tttt) cc_final: 0.3422 (tptp) REVERT: D 100 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: E 14 MET cc_start: 0.7165 (mmm) cc_final: 0.6720 (mmm) REVERT: E 61 LYS cc_start: 0.5947 (mmmm) cc_final: 0.5704 (mmmt) REVERT: E 108 GLU cc_start: 0.7297 (tp30) cc_final: 0.7051 (tp30) REVERT: F 38 HIS cc_start: 0.8043 (m-70) cc_final: 0.7789 (m-70) REVERT: F 43 GLU cc_start: 0.7838 (tt0) cc_final: 0.7535 (mt-10) REVERT: F 44 MET cc_start: 0.8758 (mtp) cc_final: 0.8448 (mtp) outliers start: 51 outliers final: 32 residues processed: 248 average time/residue: 0.1088 time to fit residues: 35.7478 Evaluate side-chains 239 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 128 ARG 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 208 ARG 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 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 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 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 Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN C 92 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132118 restraints weight = 14893.894| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.75 r_work: 0.3593 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5364 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= 0.218 Angle : 0.739 8.764 13262 Z= 0.395 Chirality : 0.045 0.231 1542 Planarity : 0.006 0.057 1327 Dihedral : 22.284 179.088 2467 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.97 % Favored : 91.34 % Rotamer: Outliers : 5.71 % Allowed : 27.89 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.74 (0.27), residues: 866 helix: -0.44 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -3.17 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 119 TYR 0.024 0.002 TYR C 28 PHE 0.039 0.003 PHE C 80 TRP 0.010 0.002 TRP A 318 HIS 0.012 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 9484) covalent geometry : angle 0.73918 / 0.40 (13262) hydrogen bonds : bond 0.06676 / 4.34 ( 545) hydrogen bonds : angle 5.39433 / 3.77 ( 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 249 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4262 (OUTLIER) cc_final: 0.3355 (mmt) REVERT: A 20 ASP cc_start: 0.8193 (m-30) cc_final: 0.7803 (t0) REVERT: A 84 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7899 (mtm180) REVERT: A 128 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6227 (ttm-80) REVERT: A 143 PHE cc_start: 0.7971 (m-10) cc_final: 0.7676 (m-10) REVERT: A 156 ASP cc_start: 0.7171 (m-30) cc_final: 0.6786 (m-30) REVERT: A 165 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8117 (mtp180) REVERT: A 256 ARG cc_start: 0.5779 (mtp-110) cc_final: 0.5280 (ttp80) REVERT: A 300 LEU cc_start: 0.8462 (mm) cc_final: 0.8105 (mt) REVERT: B 22 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7428 (mtm110) REVERT: B 42 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.6600 (ttm-80) REVERT: B 69 TYR cc_start: 0.7366 (m-80) cc_final: 0.6978 (m-80) REVERT: B 98 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7449 (mt0) REVERT: C 19 ARG cc_start: 0.7517 (tpp80) cc_final: 0.7157 (tpp80) REVERT: C 90 LYS cc_start: 0.3626 (tttt) cc_final: 0.3361 (tptp) REVERT: D 100 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: E 14 MET cc_start: 0.7187 (mmm) cc_final: 0.6515 (mmm) REVERT: E 61 LYS cc_start: 0.6070 (mmmm) cc_final: 0.5858 (mmmt) REVERT: F 43 GLU cc_start: 0.7854 (tt0) cc_final: 0.7539 (mt-10) REVERT: F 72 ASP cc_start: 0.8646 (t0) cc_final: 0.7948 (t0) outliers start: 42 outliers final: 28 residues processed: 238 average time/residue: 0.1214 time to fit residues: 37.8766 Evaluate side-chains 230 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 84 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 128 ARG 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 208 ARG 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 62 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.161258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133671 restraints weight = 14928.149| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.74 r_work: 0.3611 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9484 Z= 0.201 Angle : 0.754 8.824 13262 Z= 0.401 Chirality : 0.046 0.342 1542 Planarity : 0.006 0.049 1327 Dihedral : 22.212 179.612 2465 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 29.09 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.51 % Favored : 91.80 % Rotamer: Outliers : 5.03 % Allowed : 28.57 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.74 (0.27), residues: 866 helix: -0.43 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -3.31 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 119 TYR 0.027 0.003 TYR A 213 PHE 0.063 0.003 PHE A 287 TRP 0.010 0.002 TRP D 116 HIS 0.013 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 9484) covalent geometry : angle 0.75398 / 0.40 (13262) hydrogen bonds : bond 0.06523 / 4.25 ( 545) hydrogen bonds : angle 5.40713 / 3.79 ( 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: 37 poor density : 210 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4235 (OUTLIER) cc_final: 0.3329 (mmt) REVERT: A 20 ASP cc_start: 0.8146 (m-30) cc_final: 0.7601 (t0) REVERT: A 83 ASP cc_start: 0.8226 (m-30) cc_final: 0.7973 (m-30) REVERT: A 84 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7878 (mtm180) REVERT: A 128 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6258 (ttm-80) REVERT: A 143 PHE cc_start: 0.7788 (m-10) cc_final: 0.7519 (m-10) REVERT: A 156 ASP cc_start: 0.7133 (m-30) cc_final: 0.6718 (m-30) REVERT: A 165 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8089 (mtp180) REVERT: A 256 ARG cc_start: 0.5553 (mtp-110) cc_final: 0.5081 (ttp80) REVERT: B 22 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7468 (mtm110) REVERT: B 42 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.6623 (ttm-80) REVERT: B 69 TYR cc_start: 0.7220 (m-80) cc_final: 0.6820 (m-80) REVERT: B 98 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7461 (mt0) REVERT: C 90 LYS cc_start: 0.3648 (tttt) cc_final: 0.3392 (tptp) REVERT: E 14 MET cc_start: 0.7217 (mmm) cc_final: 0.6618 (mmm) REVERT: E 101 THR cc_start: 0.7776 (p) cc_final: 0.7422 (t) REVERT: F 38 HIS cc_start: 0.8023 (m-70) cc_final: 0.7692 (m-70) REVERT: F 43 GLU cc_start: 0.7806 (tt0) cc_final: 0.7505 (mt-10) REVERT: F 72 ASP cc_start: 0.8630 (t0) cc_final: 0.8402 (t0) outliers start: 37 outliers final: 24 residues processed: 236 average time/residue: 0.1271 time to fit residues: 39.1146 Evaluate side-chains 225 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 84 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 128 ARG 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 208 ARG 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 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.162636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135771 restraints weight = 14709.191| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.67 r_work: 0.3633 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9484 Z= 0.201 Angle : 0.754 12.369 13262 Z= 0.400 Chirality : 0.045 0.226 1542 Planarity : 0.006 0.049 1327 Dihedral : 22.100 179.965 2460 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.85 % Favored : 91.45 % Rotamer: Outliers : 4.90 % Allowed : 28.57 % Favored : 66.53 % 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: -1.70 (0.27), residues: 866 helix: -0.43 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -3.21 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 122 TYR 0.024 0.002 TYR C 28 PHE 0.046 0.003 PHE C 80 TRP 0.034 0.002 TRP A 318 HIS 0.010 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 9484) covalent geometry : angle 0.75427 / 0.40 (13262) hydrogen bonds : bond 0.06469 / 4.23 ( 545) hydrogen bonds : angle 5.36933 / 3.76 ( 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 243 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4253 (OUTLIER) cc_final: 0.3355 (mmt) REVERT: A 20 ASP cc_start: 0.8048 (m-30) cc_final: 0.7677 (t70) REVERT: A 128 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.6176 (ttm-80) REVERT: A 143 PHE cc_start: 0.7690 (m-10) cc_final: 0.7423 (m-10) REVERT: A 156 ASP cc_start: 0.7003 (m-30) cc_final: 0.6584 (m-30) REVERT: A 165 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8164 (mtp180) REVERT: A 256 ARG cc_start: 0.5369 (mtp-110) cc_final: 0.5023 (ttp80) REVERT: B 42 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8433 (ttm110) REVERT: B 69 TYR cc_start: 0.7205 (m-80) cc_final: 0.6820 (m-80) REVERT: C 19 ARG cc_start: 0.7265 (tpp80) cc_final: 0.6960 (tpp80) REVERT: E 14 MET cc_start: 0.7204 (mmm) cc_final: 0.6620 (mmm) REVERT: E 101 THR cc_start: 0.7631 (p) cc_final: 0.7296 (t) REVERT: F 38 HIS cc_start: 0.8046 (m-70) cc_final: 0.7845 (m-70) REVERT: F 43 GLU cc_start: 0.7825 (tt0) cc_final: 0.7477 (mt-10) REVERT: F 72 ASP cc_start: 0.8539 (t0) cc_final: 0.8318 (t0) outliers start: 36 outliers final: 22 residues processed: 231 average time/residue: 0.1258 time to fit residues: 38.0691 Evaluate side-chains 221 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 128 ARG 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 208 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 300 LEU 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 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE 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: 0.2980 chunk 24 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.163388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136437 restraints weight = 14763.708| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.68 r_work: 0.3643 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9484 Z= 0.198 Angle : 0.764 10.225 13262 Z= 0.407 Chirality : 0.045 0.245 1542 Planarity : 0.006 0.049 1327 Dihedral : 22.017 179.689 2457 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.51 % Favored : 91.80 % Rotamer: Outliers : 4.35 % Allowed : 28.84 % Favored : 66.80 % 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: -0.47 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -3.21 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.027 0.002 TYR A 213 PHE 0.045 0.003 PHE A 287 TRP 0.015 0.002 TRP D 116 HIS 0.012 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 9484) covalent geometry : angle 0.76403 / 0.41 (13262) hydrogen bonds : bond 0.06406 / 4.16 ( 545) hydrogen bonds : angle 5.34288 / 3.76 ( 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: 32 poor density : 201 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4282 (OUTLIER) cc_final: 0.3402 (mmt) REVERT: A 20 ASP cc_start: 0.8043 (m-30) cc_final: 0.7713 (t70) REVERT: A 83 ASP cc_start: 0.8306 (m-30) cc_final: 0.7945 (m-30) REVERT: A 128 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.6041 (ttm-80) REVERT: A 143 PHE cc_start: 0.7681 (m-10) cc_final: 0.7465 (m-10) REVERT: A 156 ASP cc_start: 0.6982 (m-30) cc_final: 0.6523 (m-30) REVERT: A 165 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8134 (mtp180) REVERT: A 256 ARG cc_start: 0.5259 (mtp-110) cc_final: 0.4947 (ttp80) REVERT: B 42 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8445 (ttm110) REVERT: B 69 TYR cc_start: 0.7183 (m-80) cc_final: 0.6792 (m-80) REVERT: C 19 ARG cc_start: 0.7255 (tpp80) cc_final: 0.6685 (tpp80) REVERT: E 14 MET cc_start: 0.7046 (mmm) cc_final: 0.6515 (mmm) REVERT: E 101 THR cc_start: 0.7640 (p) cc_final: 0.7285 (t) REVERT: F 38 HIS cc_start: 0.8041 (m-70) cc_final: 0.7796 (m-70) REVERT: F 43 GLU cc_start: 0.7836 (tt0) cc_final: 0.7526 (mt-10) REVERT: F 72 ASP cc_start: 0.8509 (t0) cc_final: 0.8284 (t0) outliers start: 32 outliers final: 24 residues processed: 223 average time/residue: 0.1231 time to fit residues: 35.8991 Evaluate side-chains 220 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 128 ARG 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 202 HIS Chi-restraints excluded: chain A residue 208 ARG 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 C residue 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE 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: 0.1980 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138125 restraints weight = 14615.460| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.68 r_work: 0.3662 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9484 Z= 0.183 Angle : 0.754 9.314 13262 Z= 0.402 Chirality : 0.045 0.294 1542 Planarity : 0.006 0.049 1327 Dihedral : 21.978 179.571 2457 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.08 % Favored : 91.34 % Rotamer: Outliers : 3.95 % Allowed : 29.39 % Favored : 66.67 % 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: -1.65 (0.27), residues: 866 helix: -0.42 (0.19), residues: 663 sheet: -2.03 (1.56), residues: 10 loop : -3.09 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.023 0.002 TYR A 213 PHE 0.042 0.003 PHE C 80 TRP 0.027 0.002 TRP D 116 HIS 0.012 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 9484) covalent geometry : angle 0.75406 / 0.40 (13262) hydrogen bonds : bond 0.06254 / 4.06 ( 545) hydrogen bonds : angle 5.35702 / 3.81 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.35 seconds wall clock time: 36 minutes 19.22 seconds (2179.22 seconds total)