Starting phenix.real_space_refine on Mon May 12 13:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubc_42082/05_2025/8ubc_42082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubc_42082/05_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_42082/05_2025/8ubc_42082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubc_42082/05_2025/8ubc_42082.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubc_42082/05_2025/8ubc_42082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubc_42082/05_2025/8ubc_42082.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.39, per 1000 atoms: 0.70 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: 2.81 Conformation dependent library (CDL) restraints added in 882.3 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 77.5% alpha, 0.9% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.52 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: 2.87 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1234 1.31 - 1.44: 3159 1.44 - 1.56: 4848 1.56 - 1.69: 183 1.69 - 1.82: 60 Bond restraints: 9484 Sorted by residual: bond pdb=" C PHE B 45 " pdb=" O PHE B 45 " ideal model delta sigma weight residual 1.235 1.185 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" CG1 ILE B 24 " pdb=" CD1 ILE B 24 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.59e+00 bond pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" CB VAL B 53 " pdb=" CG2 VAL B 53 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.55e+00 bond pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.84e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12775 2.48 - 4.96: 411 4.96 - 7.45: 60 7.45 - 9.93: 12 9.93 - 12.41: 4 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 14 " pdb=" CA THR A 14 " pdb=" CB THR A 14 " ideal model delta sigma weight residual 111.91 100.65 11.26 1.52e+00 4.33e-01 5.49e+01 angle pdb=" N LEU A 315 " pdb=" CA LEU A 315 " pdb=" C LEU A 315 " ideal model delta sigma weight residual 112.90 107.08 5.82 1.31e+00 5.83e-01 1.97e+01 angle pdb=" N LEU A 19 " pdb=" CA LEU A 19 " pdb=" C LEU A 19 " ideal model delta sigma weight residual 112.04 105.84 6.20 1.44e+00 4.82e-01 1.85e+01 angle pdb=" N TRP A 309 " pdb=" CA TRP A 309 " pdb=" C TRP A 309 " ideal model delta sigma weight residual 113.20 107.40 5.80 1.36e+00 5.41e-01 1.82e+01 angle pdb=" CA TYR C 28 " pdb=" CB TYR C 28 " pdb=" CG TYR C 28 " ideal model delta sigma weight residual 113.90 106.25 7.65 1.80e+00 3.09e-01 1.81e+01 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 5094 35.72 - 71.44: 653 71.44 - 107.16: 56 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 5808 sinusoidal: 3250 harmonic: 2558 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -79.47 -80.53 1 1.50e+01 4.44e-03 3.56e+01 dihedral pdb=" CA GLN A 322 " pdb=" C GLN A 322 " pdb=" N TYR A 323 " pdb=" CA TYR A 323 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 5805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1272 0.066 - 0.132: 239 0.132 - 0.198: 19 0.198 - 0.264: 10 0.264 - 0.330: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" P G I 4 " pdb=" OP1 G I 4 " pdb=" OP2 G I 4 " pdb=" O5' G I 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU A 200 " pdb=" CB LEU A 200 " pdb=" CD1 LEU A 200 " pdb=" CD2 LEU A 200 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 57 " pdb=" CA ILE D 57 " pdb=" CG1 ILE D 57 " pdb=" CG2 ILE D 57 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1539 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.037 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE A 231 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 29 " -0.012 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LYS A 29 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS A 29 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.030 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.010 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 520 2.70 - 3.25: 9607 3.25 - 3.80: 19821 3.80 - 4.35: 25676 4.35 - 4.90: 35984 Nonbonded interactions: 91608 Sorted by model distance: nonbonded pdb=" O SER F 62 " pdb=" OG SER F 62 " model vdw 2.145 3.040 nonbonded pdb=" O2' A I 100 " pdb=" OP2 A I 101 " model vdw 2.195 3.040 nonbonded pdb=" NH2 ARG C 36 " pdb=" OP2 U I 3 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.246 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 ... (remaining 91603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.930 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.640 ------------------------------------------------------------------------------- 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 : 37.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP F 81 HIS 0.010 0.003 HIS A 121 PHE 0.053 0.005 PHE A 231 TYR 0.035 0.004 TYR A 213 ARG 0.017 0.002 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.23731 ( 545) hydrogen bonds : angle 10.17035 ( 1503) covalent geometry : bond 0.00737 ( 9484) covalent geometry : angle 1.05658 (13262) *********************** 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 : 0.845 Fit side-chains revert: symmetry clash 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: 0.8538 (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: 0.8140 (mt) REVERT: A 113 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6246 (mttm) REVERT: A 119 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8732 (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: 0.8319 (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: 0.8179 (mt) 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: 0.6413 (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: 0.8878 (t) REVERT: B 64 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6818 (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: 0.7168 (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: 0.8033 (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 19 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8078 (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: 0.6190 (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: 0.4326 (mmmt) outliers start: 186 outliers final: 48 residues processed: 396 average time/residue: 0.2948 time to fit residues: 147.0870 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 : 0.859 ------------------------------------------------------------------------------- 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 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 37 LYS 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 63 ASN 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 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 80 optimal weight: 0.6980 chunk 72 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.0050 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.164788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137838 restraints weight = 14672.041| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.64 r_work: 0.3665 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9484 Z= 0.235 Angle : 0.830 8.726 13262 Z= 0.434 Chirality : 0.046 0.277 1542 Planarity : 0.007 0.058 1327 Dihedral : 23.526 176.050 2606 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 1.62 % Allowed : 8.43 % Favored : 89.95 % Rotamer: Outliers : 10.75 % Allowed : 22.04 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.26), residues: 866 helix: -1.41 (0.18), residues: 668 sheet: -1.33 (1.69), residues: 12 loop : -3.34 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 15 HIS 0.008 0.002 HIS A 133 PHE 0.035 0.003 PHE C 80 TYR 0.026 0.003 TYR A 213 ARG 0.009 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.07506 ( 545) hydrogen bonds : angle 5.83296 ( 1503) covalent geometry : bond 0.00505 ( 9484) covalent geometry : angle 0.82959 (13262) *********************** 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 336 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 257 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4188 (ppp) cc_final: 0.3659 (mmt) REVERT: A 10 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: A 31 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7323 (mtt-85) REVERT: A 42 ASP cc_start: 0.7814 (p0) cc_final: 0.7599 (p0) REVERT: A 103 LEU cc_start: 0.8657 (mt) cc_final: 0.8411 (mt) REVERT: A 156 ASP cc_start: 0.7068 (m-30) cc_final: 0.6633 (m-30) REVERT: B 22 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7677 (mtm110) REVERT: C 19 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7106 (tpp80) REVERT: C 30 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8355 (mm) REVERT: C 42 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7092 (ttp-170) REVERT: C 90 LYS cc_start: 0.3719 (tttt) cc_final: 0.3511 (tptp) REVERT: C 108 GLU cc_start: 0.6921 (tt0) cc_final: 0.6665 (tp30) REVERT: D 89 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: D 100 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: D 111 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7423 (ttp80) REVERT: E 17 VAL cc_start: 0.8988 (p) cc_final: 0.8736 (t) REVERT: E 52 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: E 94 MET cc_start: 0.8095 (mtp) cc_final: 0.7839 (mtm) REVERT: F 43 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: F 44 MET cc_start: 0.8679 (mtp) cc_final: 0.8458 (mtp) outliers start: 79 outliers final: 29 residues processed: 302 average time/residue: 0.2573 time to fit residues: 101.0730 Evaluate side-chains 258 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 52 GLN 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 29 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 58 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 32 GLN E 52 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 = 0.4124 r_free = 0.4124 target = 0.161055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133412 restraints weight = 14848.898| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.78 r_work: 0.3612 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9484 Z= 0.198 Angle : 0.755 8.476 13262 Z= 0.395 Chirality : 0.044 0.277 1542 Planarity : 0.006 0.045 1327 Dihedral : 22.674 178.942 2483 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 1.27 % Allowed : 8.08 % Favored : 90.65 % Rotamer: Outliers : 7.07 % Allowed : 25.17 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.27), residues: 866 helix: -0.88 (0.19), residues: 663 sheet: -1.25 (1.53), residues: 12 loop : -3.29 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 116 HIS 0.006 0.001 HIS A 133 PHE 0.042 0.003 PHE A 287 TYR 0.019 0.002 TYR C 28 ARG 0.008 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06306 ( 545) hydrogen bonds : angle 5.49866 ( 1503) covalent geometry : bond 0.00432 ( 9484) covalent geometry : angle 0.75472 (13262) *********************** 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 296 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4402 (ppp) cc_final: 0.3950 (mmt) REVERT: A 4 ARG cc_start: 0.7287 (mmp80) cc_final: 0.6173 (mmp80) REVERT: A 10 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: A 20 ASP cc_start: 0.8135 (m-30) cc_final: 0.7679 (t0) REVERT: A 143 PHE cc_start: 0.7688 (m-10) cc_final: 0.7277 (m-10) REVERT: A 156 ASP cc_start: 0.7121 (m-30) cc_final: 0.6782 (m-30) REVERT: A 300 LEU cc_start: 0.7884 (mt) cc_final: 0.7651 (mm) REVERT: B 6 GLU cc_start: 0.7184 (pm20) cc_final: 0.6696 (pm20) REVERT: B 22 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7577 (mtm110) REVERT: B 54 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: B 69 TYR cc_start: 0.7402 (m-80) cc_final: 0.6960 (m-80) REVERT: B 94 MET cc_start: 0.6653 (mtm) cc_final: 0.6272 (mtm) REVERT: B 98 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: C 19 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7122 (tpp80) REVERT: D 100 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: D 111 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7495 (ttp80) REVERT: E 17 VAL cc_start: 0.8947 (p) cc_final: 0.8591 (t) REVERT: E 100 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6766 (mt-10) REVERT: E 113 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8412 (tp) REVERT: F 20 TYR cc_start: 0.8281 (t80) cc_final: 0.7809 (t80) REVERT: F 43 GLU cc_start: 0.7826 (tt0) cc_final: 0.7544 (mt-10) REVERT: F 44 MET cc_start: 0.8754 (mtp) cc_final: 0.8518 (mtp) REVERT: F 61 LYS cc_start: 0.6971 (mttt) cc_final: 0.6674 (mttp) REVERT: F 88 ILE cc_start: 0.7846 (tt) cc_final: 0.7625 (tt) outliers start: 52 outliers final: 33 residues processed: 275 average time/residue: 0.2440 time to fit residues: 88.5192 Evaluate side-chains 241 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 263 TYR 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 54 GLU 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 B residue 98 GLN 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 68 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 113 LEU 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 58 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135681 restraints weight = 14750.012| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.75 r_work: 0.3634 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9484 Z= 0.182 Angle : 0.723 7.892 13262 Z= 0.379 Chirality : 0.042 0.218 1542 Planarity : 0.006 0.051 1327 Dihedral : 22.407 179.525 2473 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.04 % Favored : 92.03 % Rotamer: Outliers : 6.53 % Allowed : 26.39 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.27), residues: 866 helix: -0.58 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -3.25 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 116 HIS 0.007 0.001 HIS F 38 PHE 0.049 0.003 PHE A 287 TYR 0.021 0.002 TYR C 28 ARG 0.009 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 545) hydrogen bonds : angle 5.31319 ( 1503) covalent geometry : bond 0.00402 ( 9484) covalent geometry : angle 0.72295 (13262) *********************** 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 264 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4265 (ppp) cc_final: 0.3890 (mmt) REVERT: A 4 ARG cc_start: 0.7213 (mmp80) cc_final: 0.6235 (mmp80) REVERT: A 10 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: A 156 ASP cc_start: 0.7065 (m-30) cc_final: 0.6713 (m-30) REVERT: A 300 LEU cc_start: 0.7798 (mt) cc_final: 0.7585 (mm) REVERT: B 1 MET cc_start: 0.6663 (ttp) cc_final: 0.6063 (ttp) REVERT: B 22 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7585 (mtm110) REVERT: B 42 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.6592 (ttm-80) REVERT: B 54 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: C 30 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8040 (mm) REVERT: E 17 VAL cc_start: 0.8628 (p) cc_final: 0.8422 (t) REVERT: E 89 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5487 (mt0) REVERT: F 20 TYR cc_start: 0.8270 (t80) cc_final: 0.7835 (t80) REVERT: F 38 HIS cc_start: 0.7956 (m-70) cc_final: 0.7509 (m-70) REVERT: F 43 GLU cc_start: 0.7782 (tt0) cc_final: 0.7519 (mt-10) REVERT: F 69 TYR cc_start: 0.8124 (m-10) cc_final: 0.7864 (m-10) outliers start: 48 outliers final: 26 residues processed: 248 average time/residue: 0.2527 time to fit residues: 81.5982 Evaluate side-chains 224 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 C residue 30 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** B 38 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 52 GLN 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 = 0.4115 r_free = 0.4115 target = 0.160231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131417 restraints weight = 14648.873| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.83 r_work: 0.3566 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9484 Z= 0.221 Angle : 0.732 7.793 13262 Z= 0.380 Chirality : 0.042 0.216 1542 Planarity : 0.006 0.044 1327 Dihedral : 22.314 177.930 2461 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.62 % Favored : 91.69 % Rotamer: Outliers : 6.53 % Allowed : 26.26 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 866 helix: -0.34 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -3.11 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 116 HIS 0.012 0.002 HIS C 92 PHE 0.050 0.003 PHE A 287 TYR 0.025 0.002 TYR C 28 ARG 0.004 0.001 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.06045 ( 545) hydrogen bonds : angle 5.24479 ( 1503) covalent geometry : bond 0.00496 ( 9484) covalent geometry : angle 0.73186 (13262) *********************** 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 262 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7935 (t70) cc_final: 0.7633 (m-30) REVERT: A 20 ASP cc_start: 0.8080 (m-30) cc_final: 0.7612 (t0) REVERT: A 83 ASP cc_start: 0.8314 (m-30) cc_final: 0.8092 (m-30) REVERT: A 156 ASP cc_start: 0.7219 (m-30) cc_final: 0.6804 (m-30) REVERT: A 300 LEU cc_start: 0.7889 (mt) cc_final: 0.7676 (mm) REVERT: B 22 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7492 (mtm110) REVERT: B 42 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.6717 (ttm-80) REVERT: B 54 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: B 98 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: C 19 ARG cc_start: 0.7244 (tpp-160) cc_final: 0.6936 (mmp80) REVERT: D 30 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6101 (mt) REVERT: E 14 MET cc_start: 0.6991 (mmm) cc_final: 0.6730 (mmm) REVERT: E 17 VAL cc_start: 0.8715 (p) cc_final: 0.8447 (t) REVERT: E 32 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: E 89 GLN cc_start: 0.6109 (OUTLIER) cc_final: 0.5800 (mt0) REVERT: F 43 GLU cc_start: 0.7793 (tt0) cc_final: 0.7501 (mt-10) REVERT: F 72 ASP cc_start: 0.8531 (t0) cc_final: 0.8261 (t0) outliers start: 48 outliers final: 25 residues processed: 246 average time/residue: 0.2538 time to fit residues: 82.6808 Evaluate side-chains 226 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 98 GLN 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 30 ILE Chi-restraints excluded: chain E residue 32 GLN 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 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132628 restraints weight = 14585.115| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.80 r_work: 0.3576 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5966 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= 0.198 Angle : 0.724 10.013 13262 Z= 0.376 Chirality : 0.041 0.232 1542 Planarity : 0.006 0.052 1327 Dihedral : 22.222 177.052 2456 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.16 % Favored : 92.26 % Rotamer: Outliers : 6.67 % Allowed : 26.80 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.27), residues: 866 helix: -0.25 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -3.17 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 116 HIS 0.006 0.001 HIS C 92 PHE 0.055 0.003 PHE A 287 TYR 0.024 0.002 TYR C 28 ARG 0.010 0.001 ARG F 122 Details of bonding type rmsd hydrogen bonds : bond 0.05872 ( 545) hydrogen bonds : angle 5.16142 ( 1503) covalent geometry : bond 0.00445 ( 9484) covalent geometry : angle 0.72376 (13262) *********************** 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 255 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4526 (ppp) cc_final: 0.2908 (tpt) REVERT: A 20 ASP cc_start: 0.8026 (m-30) cc_final: 0.7657 (t0) REVERT: A 143 PHE cc_start: 0.7593 (m-10) cc_final: 0.7157 (m-10) REVERT: A 156 ASP cc_start: 0.7098 (m-30) cc_final: 0.6670 (m-30) REVERT: A 165 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8121 (mtp180) REVERT: B 22 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7510 (mtm110) REVERT: B 42 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.6595 (ttm-80) REVERT: B 98 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: C 19 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.7106 (tpp-160) REVERT: C 30 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8427 (mm) REVERT: E 14 MET cc_start: 0.6959 (mmm) cc_final: 0.6689 (mmm) REVERT: E 32 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: E 101 THR cc_start: 0.7860 (p) cc_final: 0.7575 (t) REVERT: F 43 GLU cc_start: 0.7837 (tt0) cc_final: 0.7475 (mt-10) outliers start: 49 outliers final: 29 residues processed: 239 average time/residue: 0.2563 time to fit residues: 80.1216 Evaluate side-chains 225 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 316 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain C residue 30 ILE 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 18 GLU Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 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 ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138389 restraints weight = 14969.561| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.77 r_work: 0.3665 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9484 Z= 0.165 Angle : 0.699 8.690 13262 Z= 0.366 Chirality : 0.040 0.246 1542 Planarity : 0.005 0.054 1327 Dihedral : 22.063 176.874 2456 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.81 % Favored : 92.73 % Rotamer: Outliers : 6.12 % Allowed : 27.62 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 866 helix: -0.19 (0.19), residues: 659 sheet: None (None), residues: 0 loop : -3.00 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 116 HIS 0.005 0.001 HIS B 97 PHE 0.022 0.003 PHE C 80 TYR 0.023 0.002 TYR A 213 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 545) hydrogen bonds : angle 5.11971 ( 1503) covalent geometry : bond 0.00364 ( 9484) covalent geometry : angle 0.69882 (13262) *********************** 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 260 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4569 (ppp) cc_final: 0.3120 (mmt) REVERT: A 83 ASP cc_start: 0.8351 (m-30) cc_final: 0.8004 (m-30) REVERT: A 107 TYR cc_start: 0.8531 (m-80) cc_final: 0.8306 (m-80) REVERT: A 143 PHE cc_start: 0.7457 (m-10) cc_final: 0.7101 (m-10) REVERT: A 156 ASP cc_start: 0.6840 (m-30) cc_final: 0.6564 (m-30) REVERT: A 165 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8098 (mtp180) REVERT: B 22 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7494 (mtm110) REVERT: B 42 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.6697 (ttm-80) REVERT: B 54 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 98 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: C 19 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.6869 (tpp-160) REVERT: C 30 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 72 ASP cc_start: 0.7165 (t0) cc_final: 0.6849 (t0) REVERT: C 98 GLN cc_start: 0.7626 (tt0) cc_final: 0.7303 (tt0) REVERT: E 14 MET cc_start: 0.6909 (mmm) cc_final: 0.6609 (mmm) REVERT: E 32 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: E 101 THR cc_start: 0.7756 (p) cc_final: 0.7475 (t) REVERT: F 43 GLU cc_start: 0.7629 (tt0) cc_final: 0.7289 (mt-10) REVERT: F 72 ASP cc_start: 0.8444 (t0) cc_final: 0.8219 (t0) outliers start: 45 outliers final: 29 residues processed: 241 average time/residue: 0.2483 time to fit residues: 77.9486 Evaluate side-chains 231 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 115 THR 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 222 ASP Chi-restraints excluded: chain A residue 254 VAL 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 98 GLN Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 30 ILE 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 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 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 98 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.163951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135766 restraints weight = 15250.824| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.83 r_work: 0.3629 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9484 Z= 0.197 Angle : 0.728 8.122 13262 Z= 0.381 Chirality : 0.041 0.251 1542 Planarity : 0.005 0.044 1327 Dihedral : 22.018 177.714 2456 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.39 % Favored : 92.26 % Rotamer: Outliers : 5.31 % Allowed : 29.66 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 866 helix: -0.20 (0.19), residues: 659 sheet: -2.10 (1.48), residues: 10 loop : -2.81 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 116 HIS 0.008 0.001 HIS A 121 PHE 0.053 0.003 PHE A 287 TYR 0.022 0.002 TYR D 26 ARG 0.007 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05870 ( 545) hydrogen bonds : angle 5.18787 ( 1503) covalent geometry : bond 0.00448 ( 9484) covalent geometry : angle 0.72847 (13262) *********************** 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 236 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4444 (ppp) cc_final: 0.3224 (mmt) REVERT: A 83 ASP cc_start: 0.8419 (m-30) cc_final: 0.8099 (m-30) REVERT: A 143 PHE cc_start: 0.7499 (m-10) cc_final: 0.7135 (m-10) REVERT: A 156 ASP cc_start: 0.6854 (m-30) cc_final: 0.6641 (m-30) REVERT: A 165 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8131 (mtp180) REVERT: A 186 SER cc_start: 0.8993 (m) cc_final: 0.8495 (p) REVERT: A 213 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: B 22 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7486 (mtm110) REVERT: B 42 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.6776 (ttm-80) REVERT: B 54 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: C 19 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6970 (tpp-160) REVERT: C 26 TYR cc_start: 0.8371 (t80) cc_final: 0.8145 (t80) REVERT: C 72 ASP cc_start: 0.7269 (t0) cc_final: 0.7020 (t0) REVERT: E 14 MET cc_start: 0.7007 (mmm) cc_final: 0.6734 (mmm) REVERT: E 32 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: F 43 GLU cc_start: 0.7709 (tt0) cc_final: 0.7338 (mt-10) REVERT: F 72 ASP cc_start: 0.8555 (t0) cc_final: 0.8314 (t0) outliers start: 39 outliers final: 24 residues processed: 223 average time/residue: 0.2671 time to fit residues: 76.8307 Evaluate side-chains 211 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU 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 213 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 254 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.163345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136252 restraints weight = 14757.347| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.70 r_work: 0.3631 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9484 Z= 0.201 Angle : 0.741 9.297 13262 Z= 0.389 Chirality : 0.041 0.256 1542 Planarity : 0.006 0.045 1327 Dihedral : 21.988 177.948 2454 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.27 % Favored : 92.38 % Rotamer: Outliers : 4.35 % Allowed : 29.93 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 866 helix: -0.21 (0.19), residues: 662 sheet: -1.72 (1.48), residues: 10 loop : -2.80 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 116 HIS 0.008 0.001 HIS A 121 PHE 0.052 0.003 PHE A 287 TYR 0.029 0.002 TYR A 107 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 545) hydrogen bonds : angle 5.24425 ( 1503) covalent geometry : bond 0.00457 ( 9484) covalent geometry : angle 0.74101 (13262) *********************** 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 226 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4314 (ppp) cc_final: 0.3385 (mmt) REVERT: A 83 ASP cc_start: 0.8329 (m-30) cc_final: 0.8012 (m-30) REVERT: A 143 PHE cc_start: 0.7475 (m-10) cc_final: 0.7147 (m-10) REVERT: A 165 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8184 (mtp180) REVERT: A 186 SER cc_start: 0.8986 (m) cc_final: 0.8551 (p) REVERT: B 22 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7466 (mtm110) REVERT: B 42 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6754 (ttm-80) REVERT: B 54 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: C 72 ASP cc_start: 0.7257 (t0) cc_final: 0.7048 (t0) REVERT: E 32 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: E 69 TYR cc_start: 0.7728 (m-10) cc_final: 0.7417 (m-80) REVERT: E 101 THR cc_start: 0.7624 (p) cc_final: 0.7348 (t) REVERT: F 43 GLU cc_start: 0.7804 (tt0) cc_final: 0.7434 (mt-10) REVERT: F 72 ASP cc_start: 0.8520 (t0) cc_final: 0.8270 (t0) outliers start: 32 outliers final: 25 residues processed: 215 average time/residue: 0.2540 time to fit residues: 71.2310 Evaluate side-chains 215 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 254 VAL 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 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 32 GLN 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 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.163859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136896 restraints weight = 14886.506| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.75 r_work: 0.3634 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9484 Z= 0.201 Angle : 0.759 10.292 13262 Z= 0.398 Chirality : 0.041 0.258 1542 Planarity : 0.006 0.044 1327 Dihedral : 21.947 178.046 2454 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.92 % Rotamer: Outliers : 4.08 % Allowed : 31.84 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 866 helix: -0.30 (0.19), residues: 660 sheet: -1.52 (1.51), residues: 10 loop : -2.76 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 116 HIS 0.008 0.001 HIS B 38 PHE 0.039 0.003 PHE A 260 TYR 0.025 0.002 TYR A 107 ARG 0.009 0.001 ARG F 122 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 545) hydrogen bonds : angle 5.31221 ( 1503) covalent geometry : bond 0.00469 ( 9484) covalent geometry : angle 0.75875 (13262) ********************** 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 217 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4317 (ppp) cc_final: 0.3642 (mmt) REVERT: A 83 ASP cc_start: 0.8349 (m-30) cc_final: 0.8038 (m-30) REVERT: A 143 PHE cc_start: 0.7453 (m-10) cc_final: 0.7165 (m-10) REVERT: A 156 ASP cc_start: 0.6925 (m-30) cc_final: 0.6644 (m-30) REVERT: A 186 SER cc_start: 0.8988 (m) cc_final: 0.8554 (p) REVERT: B 42 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.6799 (ttm-80) REVERT: B 54 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: B 69 TYR cc_start: 0.7218 (m-10) cc_final: 0.6944 (m-80) REVERT: C 72 ASP cc_start: 0.7266 (t0) cc_final: 0.7059 (t0) REVERT: E 32 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: E 69 TYR cc_start: 0.7730 (m-10) cc_final: 0.7426 (m-80) REVERT: E 101 THR cc_start: 0.7590 (p) cc_final: 0.7259 (t) REVERT: F 43 GLU cc_start: 0.7865 (tt0) cc_final: 0.7474 (mt-10) REVERT: F 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8281 (t0) outliers start: 30 outliers final: 26 residues processed: 205 average time/residue: 0.2476 time to fit residues: 66.8978 Evaluate side-chains 213 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 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 254 VAL 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 88 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 32 GLN 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 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 306 HIS ** C 13 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134909 restraints weight = 14916.920| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.73 r_work: 0.3610 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.6744 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= 0.232 Angle : 0.785 10.413 13262 Z= 0.410 Chirality : 0.042 0.258 1542 Planarity : 0.006 0.046 1327 Dihedral : 21.996 179.637 2454 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.62 % Favored : 92.03 % Rotamer: Outliers : 4.08 % Allowed : 31.43 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 866 helix: -0.38 (0.19), residues: 660 sheet: -1.17 (1.47), residues: 14 loop : -2.83 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 116 HIS 0.010 0.001 HIS B 38 PHE 0.045 0.003 PHE A 287 TYR 0.025 0.003 TYR A 107 ARG 0.009 0.001 ARG E 111 Details of bonding type rmsd hydrogen bonds : bond 0.06048 ( 545) hydrogen bonds : angle 5.34541 ( 1503) covalent geometry : bond 0.00544 ( 9484) covalent geometry : angle 0.78532 (13262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4415.41 seconds wall clock time: 77 minutes 53.06 seconds (4673.06 seconds total)