Starting phenix.real_space_refine on Sat Aug 23 01:44:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubc_42082/08_2025/8ubc_42082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubc_42082/08_2025/8ubc_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_2025/8ubc_42082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2025/8ubc_42082.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2025/8ubc_42082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubc_42082/08_2025/8ubc_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-2.0-5787/lib/python3.9/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: 1.53, per 1000 atoms: 0.17 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: 0.61 Conformation dependent library (CDL) restraints added in 166.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.96 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: 1.18 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1234 1.31 - 1.44: 3159 1.44 - 1.56: 4848 1.56 - 1.69: 183 1.69 - 1.82: 60 Bond restraints: 9484 Sorted by residual: bond pdb=" C PHE B 45 " pdb=" O PHE B 45 " ideal model delta sigma weight residual 1.235 1.185 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" CG1 ILE B 24 " pdb=" CD1 ILE B 24 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.59e+00 bond pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" CB VAL B 53 " pdb=" CG2 VAL B 53 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.55e+00 bond pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.84e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12775 2.48 - 4.96: 411 4.96 - 7.45: 60 7.45 - 9.93: 12 9.93 - 12.41: 4 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 14 " pdb=" CA THR A 14 " pdb=" CB THR A 14 " ideal model delta sigma weight residual 111.91 100.65 11.26 1.52e+00 4.33e-01 5.49e+01 angle pdb=" N LEU A 315 " pdb=" CA LEU A 315 " pdb=" C LEU A 315 " ideal model delta sigma weight residual 112.90 107.08 5.82 1.31e+00 5.83e-01 1.97e+01 angle pdb=" N LEU A 19 " pdb=" CA LEU A 19 " pdb=" C LEU A 19 " ideal model delta sigma weight residual 112.04 105.84 6.20 1.44e+00 4.82e-01 1.85e+01 angle pdb=" N TRP A 309 " pdb=" CA TRP A 309 " pdb=" C TRP A 309 " ideal model delta sigma weight residual 113.20 107.40 5.80 1.36e+00 5.41e-01 1.82e+01 angle pdb=" CA TYR C 28 " pdb=" CB TYR C 28 " pdb=" CG TYR C 28 " ideal model delta sigma weight residual 113.90 106.25 7.65 1.80e+00 3.09e-01 1.81e+01 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 5094 35.72 - 71.44: 653 71.44 - 107.16: 56 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 5808 sinusoidal: 3250 harmonic: 2558 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -79.47 -80.53 1 1.50e+01 4.44e-03 3.56e+01 dihedral pdb=" CA GLN A 322 " pdb=" C GLN A 322 " pdb=" N TYR A 323 " pdb=" CA TYR A 323 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 5805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1272 0.066 - 0.132: 239 0.132 - 0.198: 19 0.198 - 0.264: 10 0.264 - 0.330: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" P G I 4 " pdb=" OP1 G I 4 " pdb=" OP2 G I 4 " pdb=" O5' G I 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU A 200 " pdb=" CB LEU A 200 " pdb=" CD1 LEU A 200 " pdb=" CD2 LEU A 200 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 57 " pdb=" CA ILE D 57 " pdb=" CG1 ILE D 57 " pdb=" CG2 ILE D 57 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1539 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.037 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE A 231 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 29 " -0.012 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LYS A 29 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS A 29 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.030 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.010 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 520 2.70 - 3.25: 9607 3.25 - 3.80: 19821 3.80 - 4.35: 25676 4.35 - 4.90: 35984 Nonbonded interactions: 91608 Sorted by model distance: nonbonded pdb=" O SER F 62 " pdb=" OG SER F 62 " model vdw 2.145 3.040 nonbonded pdb=" O2' A I 100 " pdb=" OP2 A I 101 " model vdw 2.195 3.040 nonbonded pdb=" NH2 ARG C 36 " pdb=" OP2 U I 3 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.246 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 ... (remaining 91603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.090 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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= 0.324 Angle : 1.057 12.411 13262 Z= 0.567 Chirality : 0.052 0.330 1542 Planarity : 0.008 0.047 1327 Dihedral : 25.642 178.604 4158 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 37.78 Ramachandran Plot: Outliers : 4.62 % Allowed : 10.51 % Favored : 84.87 % Rotamer: Outliers : 25.31 % Allowed : 16.33 % Favored : 58.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00737 ( 9484) covalent geometry : angle 1.05658 (13262) hydrogen bonds : bond 0.23731 ( 545) hydrogen bonds : angle 10.17035 ( 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 : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6222 (mmtm) REVERT: A 7 ASN cc_start: 0.8883 (m-40) cc_final: 0.8539 (m-40) REVERT: A 23 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7771 (ptm-80) REVERT: A 103 LEU cc_start: 0.8395 (mt) cc_final: 0.8141 (mt) REVERT: A 113 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6244 (mttm) REVERT: A 119 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 157 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8178 (tttm) REVERT: A 240 GLU cc_start: 0.8606 (pt0) cc_final: 0.8320 (pp20) REVERT: A 241 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7441 (tmm160) REVERT: A 258 ILE cc_start: 0.8674 (mt) cc_final: 0.8180 (mt) REVERT: A 272 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 1 MET cc_start: 0.7104 (tmm) cc_final: 0.6865 (ttp) REVERT: B 9 LYS cc_start: 0.6888 (mtpt) cc_final: 0.6412 (mttt) REVERT: B 14 MET cc_start: 0.8785 (mtt) cc_final: 0.8565 (mtm) REVERT: B 47 LYS cc_start: 0.8210 (mttm) cc_final: 0.8001 (mtpp) REVERT: B 54 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: B 62 SER cc_start: 0.9116 (t) cc_final: 0.8879 (t) REVERT: B 64 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6817 (mm110) REVERT: B 108 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 14 MET cc_start: 0.7430 (tpt) cc_final: 0.7167 (mmt) REVERT: C 18 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8068 (tt0) REVERT: C 20 TYR cc_start: 0.8162 (t80) cc_final: 0.7623 (t80) REVERT: C 26 TYR cc_start: 0.8528 (t80) cc_final: 0.8219 (t80) REVERT: C 43 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: C 44 MET cc_start: 0.8606 (mtp) cc_final: 0.8365 (mtp) REVERT: C 52 GLN cc_start: 0.8391 (tp40) cc_final: 0.8034 (tp40) REVERT: C 82 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 52 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: D 92 HIS cc_start: 0.7554 (m-70) cc_final: 0.7147 (p-80) REVERT: D 108 GLU cc_start: 0.8391 (tt0) cc_final: 0.7939 (tp30) REVERT: E 50 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 103 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: E 108 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: F 15 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5344 (pt) REVERT: F 19 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7992 (tpp80) REVERT: F 25 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8445 (m) REVERT: F 52 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7405 (tm130) REVERT: F 54 GLU cc_start: 0.8226 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 83 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7937 (ttp-110) REVERT: F 85 LEU cc_start: 0.8650 (mt) cc_final: 0.8439 (mp) REVERT: F 119 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6191 (mtm180) REVERT: F 121 ASN cc_start: 0.8354 (m-40) cc_final: 0.8021 (m-40) REVERT: F 123 LYS cc_start: 0.4723 (OUTLIER) cc_final: 0.4327 (mmmt) outliers start: 186 outliers final: 46 residues processed: 396 average time/residue: 0.1151 time to fit residues: 57.9439 Evaluate side-chains 315 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 14 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 89 GLN ** 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** D 89 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.164762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137751 restraints weight = 14798.504| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.66 r_work: 0.3660 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9484 Z= 0.236 Angle : 0.838 8.722 13262 Z= 0.437 Chirality : 0.046 0.260 1542 Planarity : 0.007 0.056 1327 Dihedral : 23.513 176.301 2604 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 1.62 % Allowed : 8.20 % Favored : 90.18 % Rotamer: Outliers : 11.02 % Allowed : 21.77 % Favored : 67.21 % 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 aren not related in a simple way. whole: -2.96 (0.26), residues: 866 helix: -1.44 (0.18), residues: 673 sheet: -1.39 (1.65), residues: 12 loop : -3.37 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.029 0.003 TYR A 213 PHE 0.033 0.003 PHE A 231 TRP 0.023 0.002 TRP A 15 HIS 0.009 0.002 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 9484) covalent geometry : angle 0.83760 (13262) hydrogen bonds : bond 0.07221 ( 545) hydrogen bonds : angle 5.81395 ( 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 347 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3997 (ppp) cc_final: 0.3339 (tpt) REVERT: A 10 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: A 42 ASP cc_start: 0.7845 (p0) cc_final: 0.7636 (p0) REVERT: A 103 LEU cc_start: 0.8637 (mt) cc_final: 0.8372 (mt) REVERT: A 119 VAL cc_start: 0.9076 (m) cc_final: 0.8868 (p) REVERT: A 156 ASP cc_start: 0.7091 (m-30) cc_final: 0.6658 (m-30) REVERT: A 215 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7187 (p0) REVERT: B 22 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7666 (mtm110) REVERT: C 19 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7114 (tpp80) REVERT: C 30 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8383 (mm) REVERT: C 42 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7071 (ttp-170) REVERT: D 89 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: D 100 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6048 (tm-30) REVERT: D 111 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7475 (ttp80) REVERT: E 17 VAL cc_start: 0.9016 (p) cc_final: 0.8763 (t) REVERT: F 21 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: F 43 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: F 44 MET cc_start: 0.8696 (mtp) cc_final: 0.8478 (mtp) outliers start: 81 outliers final: 29 residues processed: 311 average time/residue: 0.0950 time to fit residues: 38.8749 Evaluate side-chains 264 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 146 ILE 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 215 ASP 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 65 VAL Chi-restraints excluded: chain B residue 66 SER 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 89 GLN 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 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: 0.9980 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 103 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 32 GLN F 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133286 restraints weight = 14778.605| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.75 r_work: 0.3600 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9484 Z= 0.205 Angle : 0.764 8.549 13262 Z= 0.398 Chirality : 0.044 0.303 1542 Planarity : 0.006 0.045 1327 Dihedral : 22.671 178.738 2484 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 1.27 % Allowed : 8.20 % Favored : 90.53 % Rotamer: Outliers : 6.39 % Allowed : 24.35 % Favored : 69.25 % 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 aren not related in a simple way. whole: -2.41 (0.26), residues: 866 helix: -0.96 (0.18), residues: 664 sheet: -1.99 (1.41), residues: 14 loop : -3.42 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 119 TYR 0.020 0.002 TYR C 28 PHE 0.042 0.003 PHE A 287 TRP 0.020 0.002 TRP D 116 HIS 0.007 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9484) covalent geometry : angle 0.76442 (13262) hydrogen bonds : bond 0.06408 ( 545) hydrogen bonds : angle 5.51190 ( 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 287 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4494 (ppp) cc_final: 0.4066 (mmt) REVERT: A 10 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: A 19 LEU cc_start: 0.8735 (mt) cc_final: 0.8533 (mt) REVERT: A 20 ASP cc_start: 0.8112 (m-30) cc_final: 0.7646 (t0) REVERT: A 119 VAL cc_start: 0.9101 (m) cc_final: 0.8897 (p) REVERT: A 156 ASP cc_start: 0.7129 (m-30) cc_final: 0.6765 (m-30) REVERT: B 6 GLU cc_start: 0.7188 (pm20) cc_final: 0.6735 (pm20) REVERT: B 22 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7504 (mtm110) REVERT: C 19 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7022 (tpp80) REVERT: C 42 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7069 (ttp-170) REVERT: D 100 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: D 111 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7490 (ttp80) REVERT: E 17 VAL cc_start: 0.8963 (p) cc_final: 0.8603 (t) REVERT: E 94 MET cc_start: 0.8133 (mtp) cc_final: 0.7726 (mtm) REVERT: F 43 GLU cc_start: 0.7837 (tt0) cc_final: 0.7572 (mt-10) REVERT: F 44 MET cc_start: 0.8741 (mtp) cc_final: 0.8491 (mtp) REVERT: F 61 LYS cc_start: 0.7092 (mttt) cc_final: 0.6757 (mttp) REVERT: F 88 ILE cc_start: 0.7906 (tt) cc_final: 0.7693 (tt) outliers start: 47 outliers final: 30 residues processed: 269 average time/residue: 0.1016 time to fit residues: 36.1834 Evaluate side-chains 242 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain 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 30 ILE 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 42 ARG Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 14 MET 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 F 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 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: 4.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132654 restraints weight = 14975.292| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.79 r_work: 0.3594 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5281 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= 0.211 Angle : 0.736 7.908 13262 Z= 0.383 Chirality : 0.043 0.220 1542 Planarity : 0.005 0.050 1327 Dihedral : 22.408 178.737 2477 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.16 % Favored : 91.92 % Rotamer: Outliers : 6.12 % Allowed : 25.99 % Favored : 67.89 % 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 aren not related in a simple way. whole: -2.01 (0.27), residues: 866 helix: -0.65 (0.19), residues: 666 sheet: -2.10 (1.34), residues: 14 loop : -3.40 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.023 0.002 TYR C 28 PHE 0.027 0.003 PHE C 80 TRP 0.017 0.002 TRP D 116 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9484) covalent geometry : angle 0.73612 (13262) hydrogen bonds : bond 0.06120 ( 545) hydrogen bonds : angle 5.39036 ( 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 260 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4357 (ppp) cc_final: 0.3974 (mmt) REVERT: A 10 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: A 31 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7650 (ptp-110) REVERT: A 107 TYR cc_start: 0.8240 (m-80) cc_final: 0.7491 (m-80) REVERT: A 143 PHE cc_start: 0.7730 (m-10) cc_final: 0.7255 (m-10) REVERT: A 156 ASP cc_start: 0.7134 (m-30) cc_final: 0.6766 (m-30) REVERT: B 22 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7531 (mtm110) REVERT: B 42 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.6538 (ttm-80) REVERT: B 54 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 89 GLN cc_start: 0.7205 (mt0) cc_final: 0.6891 (mt0) REVERT: B 98 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7512 (mt0) REVERT: C 19 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6931 (tpp-160) REVERT: D 30 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6250 (mt) REVERT: D 100 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: E 17 VAL cc_start: 0.8721 (p) cc_final: 0.8423 (t) REVERT: E 89 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5771 (mt0) REVERT: E 94 MET cc_start: 0.8172 (mtp) cc_final: 0.7870 (mtm) REVERT: F 38 HIS cc_start: 0.8115 (m-70) cc_final: 0.7872 (m-70) REVERT: F 43 GLU cc_start: 0.7828 (tt0) cc_final: 0.7559 (mt-10) REVERT: F 69 TYR cc_start: 0.8146 (m-10) cc_final: 0.7838 (m-10) outliers start: 45 outliers final: 29 residues processed: 248 average time/residue: 0.1124 time to fit residues: 36.7120 Evaluate side-chains 227 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 113 LEU 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 30 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 89 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 52 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN C 13 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132721 restraints weight = 14775.101| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.82 r_work: 0.3589 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.004 0.074 9484 Z= 0.198 Angle : 0.724 7.438 13262 Z= 0.376 Chirality : 0.042 0.213 1542 Planarity : 0.006 0.046 1327 Dihedral : 22.308 179.596 2464 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.51 % Favored : 91.69 % Rotamer: Outliers : 6.39 % Allowed : 25.31 % Favored : 68.30 % 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 aren not related in a simple way. whole: -1.80 (0.27), residues: 866 helix: -0.46 (0.19), residues: 658 sheet: -2.25 (1.33), residues: 14 loop : -3.37 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.023 0.002 TYR C 28 PHE 0.052 0.003 PHE A 287 TRP 0.021 0.002 TRP D 116 HIS 0.013 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9484) covalent geometry : angle 0.72386 (13262) hydrogen bonds : bond 0.05970 ( 545) hydrogen bonds : angle 5.25999 ( 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 249 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 20 ASP cc_start: 0.8130 (m-30) cc_final: 0.7725 (t0) REVERT: A 83 ASP cc_start: 0.8363 (m-30) cc_final: 0.8128 (m-30) REVERT: A 156 ASP cc_start: 0.7121 (m-30) cc_final: 0.6723 (m-30) REVERT: A 165 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8051 (mtp180) REVERT: A 300 LEU cc_start: 0.8441 (mm) cc_final: 0.8160 (pp) REVERT: A 318 TRP cc_start: 0.4632 (t60) cc_final: 0.4368 (t60) REVERT: B 22 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7525 (mtm110) REVERT: B 42 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.6537 (ttm-80) REVERT: B 54 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: C 19 ARG cc_start: 0.7159 (tpp80) cc_final: 0.6918 (tpp-160) REVERT: C 108 GLU cc_start: 0.7258 (tt0) cc_final: 0.6961 (tt0) REVERT: C 111 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6902 (mtt180) REVERT: D 30 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6298 (mt) REVERT: E 61 LYS cc_start: 0.6114 (mmmm) cc_final: 0.5677 (mmmt) REVERT: E 85 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8257 (mt) REVERT: E 89 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5736 (mt0) REVERT: F 43 GLU cc_start: 0.7840 (tt0) cc_final: 0.7534 (mt-10) REVERT: F 72 ASP cc_start: 0.8493 (t0) cc_final: 0.8225 (t0) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.1066 time to fit residues: 33.3160 Evaluate side-chains 222 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL 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 18 GLU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 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 52 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 0.0370 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.162322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133961 restraints weight = 14781.637| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.84 r_work: 0.3603 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9484 Z= 0.184 Angle : 0.712 10.512 13262 Z= 0.371 Chirality : 0.041 0.235 1542 Planarity : 0.006 0.059 1327 Dihedral : 22.128 178.539 2458 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.51 % Favored : 91.92 % Rotamer: Outliers : 6.26 % Allowed : 26.12 % Favored : 67.62 % 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 aren not related in a simple way. whole: -1.56 (0.27), residues: 866 helix: -0.29 (0.19), residues: 663 sheet: -2.22 (1.40), residues: 14 loop : -3.34 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 122 TYR 0.021 0.002 TYR C 28 PHE 0.032 0.002 PHE C 80 TRP 0.025 0.002 TRP D 116 HIS 0.008 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9484) covalent geometry : angle 0.71156 (13262) hydrogen bonds : bond 0.05822 ( 545) hydrogen bonds : angle 5.18787 ( 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 259 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4474 (ppp) cc_final: 0.3033 (mmm) REVERT: A 20 ASP cc_start: 0.8057 (m-30) cc_final: 0.7611 (t0) REVERT: A 31 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7083 (mtt-85) REVERT: A 143 PHE cc_start: 0.7435 (m-10) cc_final: 0.6989 (m-10) REVERT: A 156 ASP cc_start: 0.7004 (m-30) cc_final: 0.6599 (m-30) REVERT: A 165 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: A 256 ARG cc_start: 0.5638 (mtp-110) cc_final: 0.5223 (ttp80) REVERT: A 300 LEU cc_start: 0.8432 (mm) cc_final: 0.8169 (mt) REVERT: B 22 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7612 (mtm110) REVERT: B 42 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.6552 (ttm-80) REVERT: B 54 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: B 69 TYR cc_start: 0.7194 (m-80) cc_final: 0.6868 (m-80) REVERT: C 108 GLU cc_start: 0.7173 (tt0) cc_final: 0.6968 (pt0) REVERT: C 111 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6957 (mtt180) REVERT: D 30 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6179 (mt) REVERT: E 14 MET cc_start: 0.6893 (mmm) cc_final: 0.6512 (mmm) REVERT: E 85 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8312 (mt) REVERT: E 89 GLN cc_start: 0.6009 (OUTLIER) cc_final: 0.5728 (mt0) REVERT: F 43 GLU cc_start: 0.7845 (tt0) cc_final: 0.7479 (mt-10) REVERT: F 72 ASP cc_start: 0.8487 (t0) cc_final: 0.8227 (t0) outliers start: 46 outliers final: 31 residues processed: 242 average time/residue: 0.1026 time to fit residues: 32.3902 Evaluate side-chains 229 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 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 30 ILE Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4145 r_free = 0.4145 target = 0.162977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134667 restraints weight = 14872.217| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.85 r_work: 0.3612 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6233 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= 0.180 Angle : 0.701 8.485 13262 Z= 0.366 Chirality : 0.041 0.244 1542 Planarity : 0.005 0.043 1327 Dihedral : 22.059 177.287 2457 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.39 % Favored : 92.15 % Rotamer: Outliers : 6.26 % Allowed : 25.99 % 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 aren not related in a simple way. whole: -1.38 (0.27), residues: 866 helix: -0.19 (0.19), residues: 663 sheet: -2.16 (1.40), residues: 14 loop : -3.15 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 119 TYR 0.022 0.002 TYR C 28 PHE 0.056 0.003 PHE A 287 TRP 0.029 0.002 TRP D 116 HIS 0.009 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9484) covalent geometry : angle 0.70067 (13262) hydrogen bonds : bond 0.05800 ( 545) hydrogen bonds : angle 5.14603 ( 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 246 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4596 (ppp) cc_final: 0.3119 (tpt) REVERT: A 83 ASP cc_start: 0.8446 (m-30) cc_final: 0.8057 (m-30) REVERT: A 143 PHE cc_start: 0.7479 (m-10) cc_final: 0.7070 (m-10) REVERT: A 156 ASP cc_start: 0.6988 (m-30) cc_final: 0.6549 (m-30) REVERT: A 165 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: A 256 ARG cc_start: 0.5469 (mtp-110) cc_final: 0.5077 (ttp80) REVERT: A 300 LEU cc_start: 0.8300 (mm) cc_final: 0.8068 (mt) REVERT: B 22 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7509 (mtm110) REVERT: B 42 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6625 (ttm-80) REVERT: B 54 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 108 GLU cc_start: 0.7209 (tt0) cc_final: 0.6992 (tt0) REVERT: D 30 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6083 (mt) REVERT: E 14 MET cc_start: 0.6882 (mmm) cc_final: 0.6520 (mmm) REVERT: E 85 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8230 (mt) REVERT: E 89 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5650 (mt0) REVERT: F 20 TYR cc_start: 0.8274 (t80) cc_final: 0.7799 (t80) REVERT: F 38 HIS cc_start: 0.8012 (m-70) cc_final: 0.7727 (m-70) REVERT: F 43 GLU cc_start: 0.7834 (tt0) cc_final: 0.7452 (mt-10) outliers start: 46 outliers final: 30 residues processed: 234 average time/residue: 0.1130 time to fit residues: 34.7470 Evaluate side-chains 226 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 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 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 113 LEU 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 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 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 52 GLN Chi-restraints excluded: chain F residue 94 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136483 restraints weight = 14783.788| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.72 r_work: 0.3628 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.6455 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= 0.186 Angle : 0.708 7.837 13262 Z= 0.372 Chirality : 0.041 0.252 1542 Planarity : 0.005 0.042 1327 Dihedral : 22.019 176.387 2457 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.04 % Favored : 92.61 % Rotamer: Outliers : 6.12 % Allowed : 27.21 % Favored : 66.67 % 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 aren not related in a simple way. whole: -1.40 (0.27), residues: 866 helix: -0.24 (0.19), residues: 655 sheet: -2.18 (1.43), residues: 14 loop : -2.89 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 119 TYR 0.022 0.002 TYR C 28 PHE 0.028 0.002 PHE C 80 TRP 0.039 0.002 TRP D 116 HIS 0.010 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9484) covalent geometry : angle 0.70833 (13262) hydrogen bonds : bond 0.05809 ( 545) hydrogen bonds : angle 5.16891 ( 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 244 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4403 (ppp) cc_final: 0.3297 (mmt) REVERT: A 20 ASP cc_start: 0.7890 (m-30) cc_final: 0.7499 (t0) REVERT: A 31 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7634 (mtt-85) REVERT: A 83 ASP cc_start: 0.8401 (m-30) cc_final: 0.8073 (m-30) REVERT: A 143 PHE cc_start: 0.7471 (m-10) cc_final: 0.7126 (m-10) REVERT: A 156 ASP cc_start: 0.6857 (m-30) cc_final: 0.6555 (m-30) REVERT: A 165 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8105 (mtp180) REVERT: A 186 SER cc_start: 0.9010 (m) cc_final: 0.8549 (p) REVERT: A 300 LEU cc_start: 0.8346 (mm) cc_final: 0.8098 (mt) REVERT: B 22 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7520 (mtm110) REVERT: B 42 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6754 (ttm-80) REVERT: B 54 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: E 14 MET cc_start: 0.7038 (mmm) cc_final: 0.6684 (mmm) REVERT: E 32 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: E 85 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8305 (mt) REVERT: E 89 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5574 (mt0) REVERT: F 38 HIS cc_start: 0.7883 (m-70) cc_final: 0.7351 (m-70) REVERT: F 43 GLU cc_start: 0.7867 (tt0) cc_final: 0.7476 (mt-10) outliers start: 45 outliers final: 29 residues processed: 228 average time/residue: 0.1203 time to fit residues: 35.8634 Evaluate side-chains 227 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 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 215 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 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 = 0.162982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136232 restraints weight = 14851.054| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.70 r_work: 0.3628 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9484 Z= 0.200 Angle : 0.731 7.402 13262 Z= 0.386 Chirality : 0.042 0.255 1542 Planarity : 0.006 0.046 1327 Dihedral : 21.939 176.061 2452 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.16 % Favored : 92.49 % Rotamer: Outliers : 5.31 % Allowed : 27.89 % Favored : 66.80 % 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 aren not related in a simple way. whole: -1.36 (0.27), residues: 866 helix: -0.22 (0.19), residues: 658 sheet: -2.08 (1.44), residues: 14 loop : -2.87 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 119 TYR 0.025 0.002 TYR C 28 PHE 0.054 0.003 PHE A 287 TRP 0.041 0.002 TRP D 116 HIS 0.015 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9484) covalent geometry : angle 0.73143 (13262) hydrogen bonds : bond 0.05894 ( 545) hydrogen bonds : angle 5.22806 ( 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 231 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4385 (ppp) cc_final: 0.3388 (mmt) REVERT: A 20 ASP cc_start: 0.7969 (m-30) cc_final: 0.7638 (t0) REVERT: A 83 ASP cc_start: 0.8413 (m-30) cc_final: 0.8093 (m-30) REVERT: A 143 PHE cc_start: 0.7473 (m-10) cc_final: 0.7180 (m-10) REVERT: A 156 ASP cc_start: 0.6963 (m-30) cc_final: 0.6642 (m-30) REVERT: A 165 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: A 186 SER cc_start: 0.9006 (m) cc_final: 0.8560 (p) REVERT: A 300 LEU cc_start: 0.8440 (mm) cc_final: 0.8166 (mt) REVERT: B 22 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7527 (mtm110) REVERT: B 42 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.6756 (ttm-80) REVERT: B 54 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: B 69 TYR cc_start: 0.7267 (m-80) cc_final: 0.6983 (m-80) REVERT: E 14 MET cc_start: 0.7009 (mmm) cc_final: 0.6763 (mmm) REVERT: E 32 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: E 69 TYR cc_start: 0.7703 (m-80) cc_final: 0.7397 (m-80) REVERT: E 89 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5617 (mt0) REVERT: F 43 GLU cc_start: 0.7826 (tt0) cc_final: 0.7442 (mt-10) REVERT: F 72 ASP cc_start: 0.8465 (t0) cc_final: 0.8167 (t0) REVERT: F 94 MET cc_start: 0.6971 (ttp) cc_final: 0.6739 (mtp) outliers start: 39 outliers final: 28 residues processed: 219 average time/residue: 0.1194 time to fit residues: 34.4569 Evaluate side-chains 223 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 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 215 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 113 LEU 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 32 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 89 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 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137392 restraints weight = 14875.212| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.73 r_work: 0.3642 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9484 Z= 0.180 Angle : 0.724 7.420 13262 Z= 0.384 Chirality : 0.041 0.259 1542 Planarity : 0.005 0.044 1327 Dihedral : 21.826 176.012 2452 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.16 % Favored : 92.38 % Rotamer: Outliers : 4.76 % Allowed : 28.57 % Favored : 66.67 % 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 aren not related in a simple way. whole: -1.29 (0.27), residues: 866 helix: -0.19 (0.19), residues: 659 sheet: None (None), residues: 0 loop : -2.80 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 111 TYR 0.020 0.002 TYR C 28 PHE 0.054 0.003 PHE A 287 TRP 0.051 0.002 TRP D 116 HIS 0.008 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9484) covalent geometry : angle 0.72395 (13262) hydrogen bonds : bond 0.05770 ( 545) hydrogen bonds : angle 5.20136 ( 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 237 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4543 (ppp) cc_final: 0.3783 (mmt) REVERT: A 31 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7491 (mtt-85) REVERT: A 83 ASP cc_start: 0.8430 (m-30) cc_final: 0.8131 (m-30) REVERT: A 143 PHE cc_start: 0.7387 (m-10) cc_final: 0.7086 (m-10) REVERT: A 165 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8036 (mtp180) REVERT: A 186 SER cc_start: 0.9015 (m) cc_final: 0.8581 (p) REVERT: A 300 LEU cc_start: 0.8373 (mm) cc_final: 0.8136 (mt) REVERT: B 42 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.6742 (ttm-80) REVERT: B 54 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: B 69 TYR cc_start: 0.7231 (m-80) cc_final: 0.6960 (m-80) REVERT: E 14 MET cc_start: 0.6853 (mmm) cc_final: 0.6607 (mmm) REVERT: E 32 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: E 69 TYR cc_start: 0.7679 (m-80) cc_final: 0.7368 (m-80) REVERT: E 89 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5532 (mt0) REVERT: F 21 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6715 (mm-30) REVERT: F 43 GLU cc_start: 0.7789 (tt0) cc_final: 0.7436 (mt-10) REVERT: F 72 ASP cc_start: 0.8413 (t0) cc_final: 0.8138 (t0) REVERT: F 94 MET cc_start: 0.6785 (ttp) cc_final: 0.6567 (mtp) outliers start: 35 outliers final: 25 residues processed: 227 average time/residue: 0.1357 time to fit residues: 39.4926 Evaluate side-chains 219 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 215 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 89 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 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136741 restraints weight = 14606.624| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.71 r_work: 0.3629 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9484 Z= 0.200 Angle : 0.750 7.137 13262 Z= 0.396 Chirality : 0.042 0.257 1542 Planarity : 0.006 0.044 1327 Dihedral : 21.796 175.852 2450 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.62 % Favored : 92.03 % Rotamer: Outliers : 4.49 % Allowed : 28.84 % Favored : 66.67 % 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 aren not related in a simple way. whole: -1.29 (0.28), residues: 866 helix: -0.21 (0.19), residues: 663 sheet: -1.86 (1.47), residues: 14 loop : -2.76 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 119 TYR 0.021 0.002 TYR D 26 PHE 0.053 0.003 PHE A 287 TRP 0.051 0.002 TRP D 116 HIS 0.007 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9484) covalent geometry : angle 0.74974 (13262) hydrogen bonds : bond 0.05882 ( 545) hydrogen bonds : angle 5.24197 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.91 seconds wall clock time: 34 minutes 30.86 seconds (2070.86 seconds total)