Starting phenix.real_space_refine on Tue Mar 3 22:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk6_25174/03_2026/7sk6_25174.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 S 31 5.16 5 C 3052 2.51 5 N 766 2.21 5 O 833 1.98 5 H 4462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4799 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 987 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1507 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1851 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 1.74, per 1000 atoms: 0.19 Number of scatterers: 9144 At special positions: 0 Unit cell: (61.56, 66.96, 128.52, 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 31 16.00 O 833 8.00 N 766 7.00 C 3052 6.00 H 4462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.02 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 198.5 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1118 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 46.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 39 through 76 removed outlier: 3.837A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.748A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 4.041A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 4.074A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.519A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.184A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.963A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.719A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix removed outlier: 3.748A pdb=" N TYR A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'B' and resid 2 through 7 removed outlier: 4.035A pdb=" N TYR B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'F' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.510A pdb=" N VAL B 49 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.537A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.734A pdb=" N TYR A 195 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.754A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.608A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4452 1.04 - 1.24: 594 1.24 - 1.43: 1575 1.43 - 1.63: 2607 1.63 - 1.83: 42 Bond restraints: 9270 Sorted by residual: bond pdb=" ND1 HIS A 248 " pdb=" CE1 HIS A 248 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" ND1 HIS A 107 " pdb=" CE1 HIS A 107 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.29e+01 bond pdb=" ND1 HIS A 269 " pdb=" CE1 HIS A 269 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" ND1 HIS A 203 " pdb=" CE1 HIS A 203 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" ND1 HIS A 291 " pdb=" CE1 HIS A 291 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 ... (remaining 9265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 14523 2.10 - 4.19: 1742 4.19 - 6.29: 311 6.29 - 8.38: 33 8.38 - 10.48: 7 Bond angle restraints: 16616 Sorted by residual: angle pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N PRO A 98 " ideal model delta sigma weight residual 120.83 125.23 -4.40 6.10e-01 2.69e+00 5.20e+01 angle pdb=" N LYS F 79 " pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 108.90 98.42 10.48 1.63e+00 3.76e-01 4.13e+01 angle pdb=" N VAL B 39 " pdb=" CA VAL B 39 " pdb=" C VAL B 39 " ideal model delta sigma weight residual 108.81 98.54 10.27 1.62e+00 3.81e-01 4.02e+01 angle pdb=" C ILE A 210 " pdb=" N GLY A 211 " pdb=" CA GLY A 211 " ideal model delta sigma weight residual 119.99 126.87 -6.88 1.13e+00 7.83e-01 3.70e+01 angle pdb=" C ILE A 205 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " ideal model delta sigma weight residual 120.79 129.21 -8.42 1.39e+00 5.18e-01 3.67e+01 ... (remaining 16611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4238 17.49 - 34.97: 148 34.97 - 52.46: 48 52.46 - 69.95: 35 69.95 - 87.43: 4 Dihedral angle restraints: 4473 sinusoidal: 2317 harmonic: 2156 Sorted by residual: dihedral pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CA HIS A 281 " pdb=" CB HIS A 281 " ideal model delta harmonic sigma weight residual 122.80 133.20 -10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA THR A 147 " pdb=" C THR A 147 " pdb=" N TYR A 148 " pdb=" CA TYR A 148 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C ILE A 146 " pdb=" N ILE A 146 " pdb=" CA ILE A 146 " pdb=" CB ILE A 146 " ideal model delta harmonic sigma weight residual -122.00 -131.85 9.85 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 4470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 480 0.093 - 0.186: 203 0.186 - 0.279: 51 0.279 - 0.373: 10 0.373 - 0.466: 3 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA HIS A 281 " pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CB HIS A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA THR A 300 " pdb=" N THR A 300 " pdb=" C THR A 300 " pdb=" CB THR A 300 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN A 127 " pdb=" N ASN A 127 " pdb=" C ASN A 127 " pdb=" CB ASN A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 744 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 109 " -0.146 2.00e-02 2.50e+03 5.67e-02 1.29e+02 pdb=" CG TRP F 109 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 109 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP F 109 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP F 109 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 109 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 109 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 109 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 TRP F 109 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP F 109 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP F 109 " 0.008 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 109 " -0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 109 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP F 109 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 83 " 0.094 2.00e-02 2.50e+03 4.09e-02 5.01e+01 pdb=" CG TYR F 83 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR F 83 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR F 83 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 83 " 0.077 2.00e-02 2.50e+03 pdb=" HD1 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 83 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR F 83 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 322 " -0.093 2.00e-02 2.50e+03 3.92e-02 4.62e+01 pdb=" CG TYR A 322 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 322 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 322 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 322 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 322 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 322 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 322 " 0.001 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 584 2.25 - 2.83: 19486 2.83 - 3.42: 24520 3.42 - 4.01: 32883 4.01 - 4.60: 49936 Nonbonded interactions: 127409 Sorted by model distance: nonbonded pdb=" H THR A 150 " pdb=" H ASN A 151 " model vdw 1.658 2.100 nonbonded pdb=" H ASN B 45 " pdb=" H ASN B 46 " model vdw 1.661 2.100 nonbonded pdb=" H ALA E 52 " pdb=" H SER E 53 " model vdw 1.689 2.100 nonbonded pdb=" H SER E 53 " pdb=" H SER E 54 " model vdw 1.705 2.100 nonbonded pdb=" H LYS B 54 " pdb=" H LEU B 55 " model vdw 1.727 2.100 ... (remaining 127404 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 3.250 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 : 0.018 0.045 4813 Z= 1.144 Angle : 1.922 10.476 6555 Z= 1.308 Chirality : 0.111 0.466 747 Planarity : 0.014 0.089 796 Dihedral : 13.164 87.433 1684 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.20 % Favored : 94.05 % Rotamer: Outliers : 0.76 % Allowed : 1.71 % Favored : 97.53 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.36), residues: 571 helix: 2.83 (0.32), residues: 245 sheet: -1.42 (0.46), residues: 117 loop : -2.05 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 12 TYR 0.093 0.016 TYR F 83 PHE 0.068 0.012 PHE E 99 TRP 0.140 0.016 TRP F 109 HIS 0.007 0.002 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.01808 ( 4808) covalent geometry : angle 1.92291 ( 6545) SS BOND : bond 0.00611 ( 5) SS BOND : angle 1.51144 ( 10) hydrogen bonds : bond 0.22523 ( 265) hydrogen bonds : angle 7.35616 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.4563 (t0) cc_final: 0.4350 (t0) outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.2043 time to fit residues: 27.5244 Evaluate side-chains 79 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN F 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.070866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.064568 restraints weight = 84611.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.066343 restraints weight = 45914.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.067535 restraints weight = 29108.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.068293 restraints weight = 20169.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.068814 restraints weight = 15130.335| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4813 Z= 0.160 Angle : 0.616 5.237 6555 Z= 0.346 Chirality : 0.043 0.166 747 Planarity : 0.005 0.043 796 Dihedral : 5.903 55.450 644 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 1.71 % Allowed : 7.41 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.35), residues: 571 helix: 2.70 (0.31), residues: 245 sheet: -1.15 (0.48), residues: 112 loop : -1.57 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 70 TYR 0.015 0.001 TYR A 322 PHE 0.028 0.002 PHE A 294 TRP 0.014 0.001 TRP B 57 HIS 0.005 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4808) covalent geometry : angle 0.61524 ( 6545) SS BOND : bond 0.00160 ( 5) SS BOND : angle 1.01058 ( 10) hydrogen bonds : bond 0.06711 ( 265) hydrogen bonds : angle 5.43182 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8603 (mm110) cc_final: 0.8102 (tm-30) REVERT: B 49 VAL cc_start: 0.8479 (m) cc_final: 0.8267 (p) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.1528 time to fit residues: 16.7365 Evaluate side-chains 79 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 7 GLN F 16 GLN F 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.069547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.063522 restraints weight = 86640.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.065236 restraints weight = 46207.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.066424 restraints weight = 28840.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.067204 restraints weight = 19616.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.067679 restraints weight = 14429.416| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4813 Z= 0.158 Angle : 0.567 6.412 6555 Z= 0.311 Chirality : 0.041 0.161 747 Planarity : 0.004 0.036 796 Dihedral : 5.054 25.085 638 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.09 % Allowed : 7.60 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.35), residues: 571 helix: 2.65 (0.32), residues: 245 sheet: -1.04 (0.51), residues: 111 loop : -1.64 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 70 TYR 0.014 0.001 TYR A 322 PHE 0.022 0.002 PHE A 294 TRP 0.012 0.001 TRP A 265 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4808) covalent geometry : angle 0.56519 ( 6545) SS BOND : bond 0.00445 ( 5) SS BOND : angle 1.21496 ( 10) hydrogen bonds : bond 0.05506 ( 265) hydrogen bonds : angle 5.17681 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8561 (t0) cc_final: 0.8129 (t0) REVERT: A 257 TYR cc_start: 0.7698 (m-10) cc_final: 0.7453 (m-10) REVERT: B 3 GLN cc_start: 0.8672 (mm110) cc_final: 0.8209 (tm-30) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.1580 time to fit residues: 15.3744 Evaluate side-chains 78 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN F 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.070175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.064164 restraints weight = 88127.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.065919 restraints weight = 46445.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.067143 restraints weight = 28478.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.067929 restraints weight = 18989.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.068403 restraints weight = 13587.460| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4813 Z= 0.113 Angle : 0.506 4.261 6555 Z= 0.274 Chirality : 0.041 0.156 747 Planarity : 0.004 0.038 796 Dihedral : 4.700 23.354 638 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.71 % Allowed : 8.17 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.36), residues: 571 helix: 2.93 (0.31), residues: 245 sheet: -1.04 (0.51), residues: 111 loop : -1.36 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 70 TYR 0.013 0.001 TYR A 322 PHE 0.017 0.002 PHE A 294 TRP 0.008 0.001 TRP F 111 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4808) covalent geometry : angle 0.50518 ( 6545) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.99114 ( 10) hydrogen bonds : bond 0.04780 ( 265) hydrogen bonds : angle 4.77630 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8671 (t0) cc_final: 0.8160 (t0) REVERT: A 179 ASP cc_start: 0.7376 (m-30) cc_final: 0.7166 (m-30) REVERT: B 3 GLN cc_start: 0.8594 (mm110) cc_final: 0.8170 (tm-30) outliers start: 9 outliers final: 9 residues processed: 77 average time/residue: 0.1491 time to fit residues: 14.6572 Evaluate side-chains 77 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.069671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.063679 restraints weight = 87292.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.065419 restraints weight = 46660.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.066566 restraints weight = 29026.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.067352 restraints weight = 19741.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.067844 restraints weight = 14404.892| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4813 Z= 0.127 Angle : 0.500 4.428 6555 Z= 0.272 Chirality : 0.040 0.154 747 Planarity : 0.004 0.038 796 Dihedral : 4.574 22.924 638 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 9.51 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.36), residues: 571 helix: 2.84 (0.31), residues: 245 sheet: -1.12 (0.51), residues: 111 loop : -1.35 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.013 0.001 TYR A 322 PHE 0.015 0.001 PHE A 294 TRP 0.008 0.001 TRP F 109 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4808) covalent geometry : angle 0.49897 ( 6545) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.96588 ( 10) hydrogen bonds : bond 0.04533 ( 265) hydrogen bonds : angle 4.71001 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8673 (mm110) cc_final: 0.8173 (tm-30) REVERT: E 5 MET cc_start: 0.7907 (mtp) cc_final: 0.7594 (mtm) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.1180 time to fit residues: 11.6999 Evaluate side-chains 69 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.069498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.063455 restraints weight = 87981.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.065183 restraints weight = 47348.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.066308 restraints weight = 29479.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.067081 restraints weight = 20245.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.067595 restraints weight = 14876.452| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4813 Z= 0.116 Angle : 0.494 4.079 6555 Z= 0.267 Chirality : 0.040 0.153 747 Planarity : 0.004 0.040 796 Dihedral : 4.458 22.234 638 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.52 % Allowed : 10.27 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.36), residues: 571 helix: 2.90 (0.31), residues: 245 sheet: -1.04 (0.51), residues: 111 loop : -1.18 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 70 TYR 0.013 0.001 TYR A 322 PHE 0.015 0.001 PHE A 294 TRP 0.007 0.001 TRP F 109 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4808) covalent geometry : angle 0.49291 ( 6545) SS BOND : bond 0.00218 ( 5) SS BOND : angle 0.88988 ( 10) hydrogen bonds : bond 0.04307 ( 265) hydrogen bonds : angle 4.62429 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7368 (m-10) cc_final: 0.7146 (m-10) REVERT: B 3 GLN cc_start: 0.8673 (mm110) cc_final: 0.8206 (tm-30) REVERT: E 5 MET cc_start: 0.7986 (mtp) cc_final: 0.7681 (mtm) outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.1231 time to fit residues: 10.7816 Evaluate side-chains 70 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN E 90 GLN F 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.068210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.062647 restraints weight = 89648.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.064232 restraints weight = 46896.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.065319 restraints weight = 28586.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.066038 restraints weight = 19366.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.066568 restraints weight = 14171.449| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4813 Z= 0.158 Angle : 0.521 4.239 6555 Z= 0.285 Chirality : 0.040 0.156 747 Planarity : 0.004 0.039 796 Dihedral : 4.564 23.233 638 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.52 % Allowed : 11.22 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.36), residues: 571 helix: 2.73 (0.32), residues: 245 sheet: -1.12 (0.52), residues: 111 loop : -1.28 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.014 0.001 TYR A 322 PHE 0.012 0.001 PHE A 294 TRP 0.011 0.001 TRP F 111 HIS 0.005 0.002 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4808) covalent geometry : angle 0.51928 ( 6545) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.08167 ( 10) hydrogen bonds : bond 0.04400 ( 265) hydrogen bonds : angle 4.69046 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7579 (m-10) cc_final: 0.7161 (m-10) REVERT: B 3 GLN cc_start: 0.8789 (mm110) cc_final: 0.8169 (tm-30) REVERT: E 5 MET cc_start: 0.8089 (mtp) cc_final: 0.7767 (mtm) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.1277 time to fit residues: 11.4516 Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.067942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.062420 restraints weight = 87946.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.063988 restraints weight = 46667.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.065046 restraints weight = 28957.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.065754 restraints weight = 19664.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.066260 restraints weight = 14441.269| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4813 Z= 0.148 Angle : 0.517 5.442 6555 Z= 0.281 Chirality : 0.040 0.153 747 Planarity : 0.004 0.040 796 Dihedral : 4.553 23.143 638 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 11.22 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.36), residues: 571 helix: 2.72 (0.32), residues: 245 sheet: -1.20 (0.52), residues: 111 loop : -1.27 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 70 TYR 0.014 0.001 TYR A 322 PHE 0.013 0.001 PHE A 294 TRP 0.013 0.001 TRP F 111 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4808) covalent geometry : angle 0.51577 ( 6545) SS BOND : bond 0.00408 ( 5) SS BOND : angle 0.98236 ( 10) hydrogen bonds : bond 0.04296 ( 265) hydrogen bonds : angle 4.67093 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7476 (m-10) cc_final: 0.7078 (m-10) REVERT: B 3 GLN cc_start: 0.8821 (mm110) cc_final: 0.8172 (tm-30) REVERT: E 5 MET cc_start: 0.8103 (mtp) cc_final: 0.7779 (mtm) outliers start: 8 outliers final: 8 residues processed: 65 average time/residue: 0.1189 time to fit residues: 10.3643 Evaluate side-chains 68 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 109 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.065557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.060393 restraints weight = 92217.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.061886 restraints weight = 47932.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.062936 restraints weight = 29030.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.063595 restraints weight = 19502.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063973 restraints weight = 14245.060| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4813 Z= 0.284 Angle : 0.648 5.058 6555 Z= 0.364 Chirality : 0.042 0.152 747 Planarity : 0.005 0.041 796 Dihedral : 5.200 26.733 638 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.52 % Allowed : 11.41 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.35), residues: 571 helix: 1.93 (0.31), residues: 245 sheet: -1.75 (0.51), residues: 106 loop : -1.83 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 70 TYR 0.016 0.002 TYR A 322 PHE 0.018 0.002 PHE A 261 TRP 0.027 0.002 TRP F 111 HIS 0.009 0.003 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 4808) covalent geometry : angle 0.64628 ( 6545) SS BOND : bond 0.00670 ( 5) SS BOND : angle 1.47013 ( 10) hydrogen bonds : bond 0.05187 ( 265) hydrogen bonds : angle 5.31233 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 MET cc_start: 0.8091 (mtp) cc_final: 0.7681 (mtp) outliers start: 8 outliers final: 8 residues processed: 61 average time/residue: 0.1194 time to fit residues: 9.9314 Evaluate side-chains 62 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS E 39 GLN F 87 ASN F 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.066581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.061084 restraints weight = 90155.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.062718 restraints weight = 46082.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.063852 restraints weight = 27578.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.064561 restraints weight = 18143.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.064951 restraints weight = 12926.689| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4813 Z= 0.137 Angle : 0.537 4.659 6555 Z= 0.292 Chirality : 0.041 0.151 747 Planarity : 0.004 0.042 796 Dihedral : 4.823 24.313 638 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.71 % Allowed : 11.79 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.36), residues: 571 helix: 2.49 (0.32), residues: 245 sheet: -1.66 (0.51), residues: 111 loop : -1.46 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 70 TYR 0.015 0.001 TYR A 322 PHE 0.015 0.001 PHE A 294 TRP 0.018 0.001 TRP F 111 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4808) covalent geometry : angle 0.53626 ( 6545) SS BOND : bond 0.00366 ( 5) SS BOND : angle 0.99847 ( 10) hydrogen bonds : bond 0.04464 ( 265) hydrogen bonds : angle 4.84118 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1278 time to fit residues: 10.7623 Evaluate side-chains 64 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.066562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.061044 restraints weight = 91326.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.062655 restraints weight = 47036.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.063803 restraints weight = 28484.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.064544 restraints weight = 18785.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.064947 restraints weight = 13345.876| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.255 4813 Z= 0.269 Angle : 1.077 59.196 6555 Z= 0.653 Chirality : 0.042 0.273 747 Planarity : 0.004 0.042 796 Dihedral : 4.818 23.941 638 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.33 % Allowed : 12.17 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.36), residues: 571 helix: 2.50 (0.32), residues: 245 sheet: -1.64 (0.51), residues: 111 loop : -1.46 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 70 TYR 0.015 0.001 TYR A 322 PHE 0.015 0.001 PHE A 294 TRP 0.017 0.001 TRP F 111 HIS 0.006 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4808) covalent geometry : angle 1.07750 ( 6545) SS BOND : bond 0.00362 ( 5) SS BOND : angle 0.99604 ( 10) hydrogen bonds : bond 0.04461 ( 265) hydrogen bonds : angle 4.84161 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.76 seconds wall clock time: 30 minutes 42.74 seconds (1842.74 seconds total)