Starting phenix.real_space_refine on Sun Jul 27 03:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_25174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_25174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_25174.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_25174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk6_25174/07_2025/7sk6_25174_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.19, per 1000 atoms: 0.57 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: 2.29 Conformation dependent library (CDL) restraints added in 813.3 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: 0.80 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: 3.47 Time building geometry restraints manager: 2.85 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: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.140 0.016 TRP F 109 HIS 0.007 0.002 HIS B 25 PHE 0.068 0.012 PHE E 99 TYR 0.093 0.016 TYR F 83 ARG 0.004 0.001 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.22523 ( 265) hydrogen bonds : angle 7.35616 ( 753) SS BOND : bond 0.00611 ( 5) SS BOND : angle 1.51144 ( 10) covalent geometry : bond 0.01808 ( 4808) covalent geometry : angle 1.92291 ( 6545) *********************** 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 : 0.717 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: symmetry clash REVERT: A 275 ASP cc_start: 0.4563 (t0) cc_final: 0.4316 (t0) outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.4417 time to fit residues: 59.9825 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 : 0.690 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 245 GLN F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.070728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.064581 restraints weight = 84288.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.066349 restraints weight = 45161.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.067598 restraints weight = 28185.355| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4813 Z= 0.161 Angle : 0.612 5.171 6555 Z= 0.342 Chirality : 0.043 0.169 747 Planarity : 0.005 0.043 796 Dihedral : 5.866 55.234 644 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 1.71 % Allowed : 7.22 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 571 helix: 2.75 (0.31), residues: 245 sheet: -1.24 (0.48), residues: 113 loop : -1.62 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 57 HIS 0.005 0.001 HIS A 281 PHE 0.026 0.002 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.006 0.001 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 265) hydrogen bonds : angle 5.37435 ( 753) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.02488 ( 10) covalent geometry : bond 0.00311 ( 4808) covalent geometry : angle 0.61129 ( 6545) *********************** 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 88 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.716 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: B 3 GLN cc_start: 0.8590 (mm110) cc_final: 0.8207 (tm-30) REVERT: B 49 VAL cc_start: 0.8463 (m) cc_final: 0.8254 (p) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.3468 time to fit residues: 37.8862 Evaluate side-chains 76 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN F 16 GLN F 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.062534 restraints weight = 88563.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064240 restraints weight = 46795.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.065437 restraints weight = 28739.927| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4813 Z= 0.228 Angle : 0.607 4.571 6555 Z= 0.344 Chirality : 0.042 0.160 747 Planarity : 0.005 0.038 796 Dihedral : 5.249 26.386 638 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.71 % Allowed : 8.56 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.34), residues: 571 helix: 2.31 (0.31), residues: 245 sheet: -1.28 (0.50), residues: 110 loop : -1.72 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 265 HIS 0.008 0.002 HIS A 307 PHE 0.019 0.002 PHE A 294 TYR 0.016 0.001 TYR A 322 ARG 0.007 0.001 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.05871 ( 265) hydrogen bonds : angle 5.43418 ( 753) SS BOND : bond 0.00538 ( 5) SS BOND : angle 1.33060 ( 10) covalent geometry : bond 0.00454 ( 4808) covalent geometry : angle 0.60523 ( 6545) *********************** 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 79 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.780 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 outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.3534 time to fit residues: 34.6729 Evaluate side-chains 75 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN F 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.068204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.062409 restraints weight = 87102.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.064045 restraints weight = 45198.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.065178 restraints weight = 28113.221| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4813 Z= 0.174 Angle : 0.556 4.077 6555 Z= 0.310 Chirality : 0.041 0.157 747 Planarity : 0.004 0.041 796 Dihedral : 5.050 25.416 638 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 9.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.35), residues: 571 helix: 2.45 (0.31), residues: 245 sheet: -1.34 (0.50), residues: 111 loop : -1.67 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 111 HIS 0.006 0.002 HIS A 307 PHE 0.016 0.002 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 265) hydrogen bonds : angle 5.24978 ( 753) SS BOND : bond 0.00490 ( 5) SS BOND : angle 1.25889 ( 10) covalent geometry : bond 0.00353 ( 4808) covalent geometry : angle 0.55407 ( 6545) *********************** 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 76 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.776 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: E 5 MET cc_start: 0.7860 (mtp) cc_final: 0.7377 (mtp) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.3518 time to fit residues: 33.3000 Evaluate side-chains 72 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.066742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.061157 restraints weight = 89326.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.062782 restraints weight = 45890.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.063906 restraints weight = 27799.638| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4813 Z= 0.206 Angle : 0.582 5.068 6555 Z= 0.325 Chirality : 0.041 0.152 747 Planarity : 0.005 0.045 796 Dihedral : 5.096 25.585 638 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.52 % Allowed : 10.65 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.35), residues: 571 helix: 2.35 (0.31), residues: 244 sheet: -1.53 (0.49), residues: 111 loop : -1.74 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 111 HIS 0.007 0.002 HIS B 25 PHE 0.014 0.002 PHE A 199 TYR 0.016 0.001 TYR A 322 ARG 0.004 0.001 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.05130 ( 265) hydrogen bonds : angle 5.25136 ( 753) SS BOND : bond 0.00496 ( 5) SS BOND : angle 1.30673 ( 10) covalent geometry : bond 0.00419 ( 4808) covalent geometry : angle 0.58023 ( 6545) *********************** 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 72 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.807 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: 0.8063 (mtp) cc_final: 0.7586 (mtm) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.2999 time to fit residues: 28.0816 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 : 0.721 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.067675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062135 restraints weight = 88564.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.063766 restraints weight = 45879.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.064882 restraints weight = 27516.666| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4813 Z= 0.121 Angle : 0.513 4.116 6555 Z= 0.281 Chirality : 0.041 0.154 747 Planarity : 0.004 0.044 796 Dihedral : 4.749 23.476 638 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.33 % Allowed : 11.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.36), residues: 571 helix: 2.71 (0.31), residues: 245 sheet: -1.42 (0.51), residues: 111 loop : -1.49 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 111 HIS 0.004 0.001 HIS A 307 PHE 0.017 0.001 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.002 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 265) hydrogen bonds : angle 4.85442 ( 753) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.95235 ( 10) covalent geometry : bond 0.00247 ( 4808) covalent geometry : angle 0.51190 ( 6545) *********************** 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 71 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.707 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 179 ASP cc_start: 0.7804 (m-30) cc_final: 0.7603 (m-30) REVERT: B 3 GLN cc_start: 0.8928 (mm110) cc_final: 0.8178 (tm-30) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.3329 time to fit residues: 30.3689 Evaluate side-chains 69 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.066714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.061302 restraints weight = 90217.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.062913 restraints weight = 46184.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064030 restraints weight = 27855.170| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4813 Z= 0.165 Angle : 0.533 4.024 6555 Z= 0.295 Chirality : 0.040 0.154 747 Planarity : 0.004 0.042 796 Dihedral : 4.778 24.176 638 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.36), residues: 571 helix: 2.56 (0.31), residues: 245 sheet: -1.45 (0.52), residues: 111 loop : -1.54 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 111 HIS 0.006 0.001 HIS B 25 PHE 0.013 0.002 PHE A 294 TYR 0.016 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 265) hydrogen bonds : angle 4.91925 ( 753) SS BOND : bond 0.00458 ( 5) SS BOND : angle 1.13359 ( 10) covalent geometry : bond 0.00338 ( 4808) covalent geometry : angle 0.53119 ( 6545) *********************** 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 69 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.788 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: E 5 MET cc_start: 0.8208 (mtp) cc_final: 0.7851 (mtm) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.3325 time to fit residues: 29.7322 Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 E residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.067732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.062216 restraints weight = 89200.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.063837 restraints weight = 45680.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.064959 restraints weight = 26670.415| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4813 Z= 0.115 Angle : 0.504 4.279 6555 Z= 0.276 Chirality : 0.041 0.160 747 Planarity : 0.004 0.041 796 Dihedral : 4.574 16.913 638 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.37), residues: 571 helix: 2.71 (0.31), residues: 245 sheet: -1.37 (0.53), residues: 111 loop : -1.33 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 111 HIS 0.004 0.001 HIS A 298 PHE 0.015 0.001 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.002 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 265) hydrogen bonds : angle 4.72290 ( 753) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.89209 ( 10) covalent geometry : bond 0.00238 ( 4808) covalent geometry : angle 0.50347 ( 6545) *********************** 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: 7 poor density : 61 time to evaluate : 0.781 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 outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.3497 time to fit residues: 30.7632 Evaluate side-chains 68 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 E residue 39 GLN Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.067860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.062317 restraints weight = 87340.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.063923 restraints weight = 44658.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065036 restraints weight = 27003.731| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4813 Z= 0.120 Angle : 0.510 4.967 6555 Z= 0.277 Chirality : 0.041 0.155 747 Planarity : 0.004 0.045 796 Dihedral : 4.561 17.648 638 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 12.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.36), residues: 571 helix: 2.72 (0.31), residues: 245 sheet: -1.29 (0.53), residues: 111 loop : -1.33 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 111 HIS 0.004 0.001 HIS A 298 PHE 0.014 0.001 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.002 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 265) hydrogen bonds : angle 4.66671 ( 753) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.93077 ( 10) covalent geometry : bond 0.00250 ( 4808) covalent geometry : angle 0.50938 ( 6545) *********************** 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 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.671 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: E 5 MET cc_start: 0.8200 (mtp) cc_final: 0.7819 (mtm) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.3762 time to fit residues: 33.9155 Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 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 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 42 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 = 0.3864 r_free = 0.3864 target = 0.068110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.062469 restraints weight = 89495.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064101 restraints weight = 45431.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.065229 restraints weight = 27597.905| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4813 Z= 0.112 Angle : 0.490 4.630 6555 Z= 0.266 Chirality : 0.040 0.154 747 Planarity : 0.004 0.046 796 Dihedral : 4.442 17.143 638 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 571 helix: 2.76 (0.31), residues: 245 sheet: -1.25 (0.53), residues: 111 loop : -1.22 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 111 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.002 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 265) hydrogen bonds : angle 4.56503 ( 753) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.87966 ( 10) covalent geometry : bond 0.00233 ( 4808) covalent geometry : angle 0.48893 ( 6545) ********************** 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 69 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.696 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: 0.8956 (mm110) cc_final: 0.8284 (tm-30) REVERT: E 5 MET cc_start: 0.8205 (mtp) cc_final: 0.7839 (mtm) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.2909 time to fit residues: 25.9365 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 : 0.799 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.0060 chunk 46 optimal weight: 0.0980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.062477 restraints weight = 88840.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064190 restraints weight = 46085.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065281 restraints weight = 27512.632| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 4813 Z= 0.254 Angle : 1.054 59.200 6555 Z= 0.643 Chirality : 0.042 0.309 747 Planarity : 0.004 0.045 796 Dihedral : 4.439 17.036 638 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.14 % Allowed : 12.36 % Favored : 86.50 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.37), residues: 571 helix: 2.77 (0.31), residues: 245 sheet: -1.24 (0.53), residues: 111 loop : -1.21 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 111 HIS 0.006 0.001 HIS F 38 PHE 0.013 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.002 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 265) hydrogen bonds : angle 4.56346 ( 753) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.87852 ( 10) covalent geometry : bond 0.00514 ( 4808) covalent geometry : angle 1.05434 ( 6545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.91 seconds wall clock time: 68 minutes 4.06 seconds (4084.06 seconds total)