Starting phenix.real_space_refine on Thu Feb 13 13:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk6_25174/02_2025/7sk6_25174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk6_25174/02_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_25174/02_2025/7sk6_25174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk6_25174/02_2025/7sk6_25174.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk6_25174/02_2025/7sk6_25174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk6_25174/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.10, per 1000 atoms: 0.56 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: 2.30 Conformation dependent library (CDL) restraints added in 839.3 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: 0.79 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: 3.50 Time building geometry restraints manager: 2.74 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: 2.680 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: 0.190 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.030 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.510 ------------------------------------------------------------------------------- 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 4808 Z= 1.167 Angle : 1.923 10.476 6545 Z= 1.309 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 *********************** 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 : 0.748 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: 0.4509 time to fit residues: 61.0275 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 : 0.732 ------------------------------------------------------------------------------- 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 = 0.070718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.064563 restraints weight = 84175.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.066340 restraints weight = 45073.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.067581 restraints weight = 28104.020| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.205 Angle : 0.611 5.171 6545 Z= 0.342 Chirality : 0.043 0.169 747 Planarity : 0.005 0.043 796 Dihedral : 5.865 55.230 644 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.14 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 0.025 0.002 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.006 0.001 ARG F 70 *********************** 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 : 0.843 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: 0.8591 (mm110) cc_final: 0.8207 (tm-30) REVERT: B 49 VAL cc_start: 0.8464 (m) cc_final: 0.8256 (p) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.3540 time to fit residues: 38.3669 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 : 0.756 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 0.5980 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: 0.7980 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 7 GLN F 16 GLN F 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.068836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.062881 restraints weight = 88392.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.064615 restraints weight = 47081.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.065820 restraints weight = 29162.462| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4808 Z= 0.262 Angle : 0.588 5.181 6545 Z= 0.330 Chirality : 0.042 0.163 747 Planarity : 0.005 0.039 796 Dihedral : 5.169 25.842 638 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.71 % Allowed : 7.98 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.35), residues: 571 helix: 2.40 (0.31), residues: 245 sheet: -1.23 (0.50), residues: 110 loop : -1.70 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 265 HIS 0.009 0.002 HIS A 307 PHE 0.020 0.002 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.008 0.001 ARG F 70 *********************** 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 : 0.719 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: 0.3278 time to fit residues: 31.7168 Evaluate side-chains 76 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3906 r_free = 0.3906 target = 0.069904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.064117 restraints weight = 87046.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.065825 restraints weight = 45242.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.067018 restraints weight = 27516.371| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4808 Z= 0.150 Angle : 0.514 4.173 6545 Z= 0.281 Chirality : 0.041 0.157 747 Planarity : 0.004 0.039 796 Dihedral : 4.754 23.762 638 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.74 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: 0.70 (0.36), residues: 571 helix: 2.83 (0.31), residues: 245 sheet: -1.15 (0.51), residues: 111 loop : -1.51 (0.38), 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 307 PHE 0.017 0.002 PHE A 294 TYR 0.013 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 *********************** 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 78 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.836 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 outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.3445 time to fit residues: 33.4907 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 : 0.828 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** B 25 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.067181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.061575 restraints weight = 88267.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.063160 restraints weight = 45486.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064278 restraints weight = 28252.227| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4808 Z= 0.307 Angle : 0.598 5.028 6545 Z= 0.338 Chirality : 0.041 0.156 747 Planarity : 0.005 0.041 796 Dihedral : 5.078 25.640 638 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.71 % Allowed : 10.65 % Favored : 87.64 % 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: 0.05 (0.35), residues: 571 helix: 2.21 (0.31), residues: 245 sheet: -1.48 (0.49), residues: 111 loop : -1.74 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 111 HIS 0.009 0.002 HIS B 25 PHE 0.015 0.002 PHE A 199 TYR 0.015 0.002 TYR A 322 ARG 0.006 0.001 ARG E 67 *********************** 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 71 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.777 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 outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.3241 time to fit residues: 28.5543 Evaluate side-chains 66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.067489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.062034 restraints weight = 88531.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.063592 restraints weight = 46094.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.064673 restraints weight = 28315.909| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4808 Z= 0.196 Angle : 0.531 4.025 6545 Z= 0.293 Chirality : 0.041 0.153 747 Planarity : 0.004 0.043 796 Dihedral : 4.831 24.084 638 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.33 % Allowed : 11.79 % Favored : 86.88 % 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: 0.37 (0.36), residues: 571 helix: 2.55 (0.32), residues: 245 sheet: -1.49 (0.50), residues: 111 loop : -1.56 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 111 HIS 0.005 0.001 HIS A 307 PHE 0.017 0.001 PHE A 294 TYR 0.015 0.001 TYR A 322 ARG 0.004 0.001 ARG F 70 *********************** 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 68 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.793 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: 0.8006 (mtp) cc_final: 0.7521 (mtm) outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.3011 time to fit residues: 26.3696 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 : 0.718 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 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: 0.8980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.067844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.062329 restraints weight = 89892.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.063945 restraints weight = 46351.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065030 restraints weight = 28081.582| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4808 Z= 0.167 Angle : 0.503 4.056 6545 Z= 0.275 Chirality : 0.040 0.154 747 Planarity : 0.004 0.042 796 Dihedral : 4.605 23.019 638 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 11.41 % Favored : 87.45 % 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: 2.72 (0.31), residues: 245 sheet: -1.30 (0.53), residues: 111 loop : -1.40 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 111 HIS 0.003 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 *********************** 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 66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.748 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: 0.8925 (mm110) cc_final: 0.8204 (tm-30) REVERT: E 5 MET cc_start: 0.8113 (mtp) cc_final: 0.7769 (mtm) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.3047 time to fit residues: 26.1776 Evaluate side-chains 64 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.067878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.062342 restraints weight = 89347.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.064000 restraints weight = 45575.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.065092 restraints weight = 27283.932| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.165 Angle : 0.500 4.163 6545 Z= 0.273 Chirality : 0.040 0.154 747 Planarity : 0.004 0.041 796 Dihedral : 4.496 22.643 638 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 11.41 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.36), residues: 571 helix: 2.76 (0.31), residues: 245 sheet: -1.34 (0.53), residues: 111 loop : -1.29 (0.41), 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 298 PHE 0.014 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 *********************** 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 66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.837 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: 0.8927 (mm110) cc_final: 0.8213 (tm-30) REVERT: E 5 MET cc_start: 0.8148 (mtp) cc_final: 0.7803 (mtm) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.3125 time to fit residues: 26.9312 Evaluate side-chains 65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.068346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.062779 restraints weight = 88616.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.064455 restraints weight = 45959.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.065589 restraints weight = 27572.947| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4808 Z= 0.144 Angle : 0.490 4.295 6545 Z= 0.266 Chirality : 0.040 0.158 747 Planarity : 0.004 0.041 796 Dihedral : 4.348 16.871 638 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.14 % Allowed : 11.98 % Favored : 86.88 % 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: 0.89 (0.37), residues: 571 helix: 2.85 (0.31), residues: 245 sheet: -1.22 (0.53), residues: 111 loop : -1.10 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 111 HIS 0.005 0.001 HIS A 281 PHE 0.013 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 *********************** 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 : 0.822 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: 0.8961 (mm110) cc_final: 0.8316 (tm-30) REVERT: E 5 MET cc_start: 0.8158 (mtp) cc_final: 0.7805 (mtm) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.3225 time to fit residues: 28.3239 Evaluate side-chains 65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.069186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.063208 restraints weight = 88381.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.064919 restraints weight = 45483.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.065994 restraints weight = 27417.491| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4808 Z= 0.149 Angle : 0.486 4.388 6545 Z= 0.263 Chirality : 0.040 0.153 747 Planarity : 0.004 0.040 796 Dihedral : 4.329 17.652 638 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.14 % Allowed : 12.17 % Favored : 86.69 % 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: 0.90 (0.37), residues: 571 helix: 2.85 (0.31), residues: 245 sheet: -1.18 (0.53), residues: 111 loop : -1.11 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 111 HIS 0.003 0.001 HIS A 269 PHE 0.012 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 ********************** 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 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.824 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: 0.8976 (mm110) cc_final: 0.8324 (tm-30) REVERT: E 5 MET cc_start: 0.8166 (mtp) cc_final: 0.7801 (mtm) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.3005 time to fit residues: 26.1028 Evaluate side-chains 65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** F 31 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 = 0.3852 r_free = 0.3852 target = 0.068301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.062643 restraints weight = 90852.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.064421 restraints weight = 46823.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065585 restraints weight = 27134.929| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4808 Z= 0.163 Angle : 0.494 4.940 6545 Z= 0.269 Chirality : 0.040 0.155 747 Planarity : 0.004 0.040 796 Dihedral : 4.313 17.263 638 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.14 % Allowed : 11.98 % Favored : 86.88 % 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: 0.89 (0.37), residues: 571 helix: 2.84 (0.31), residues: 245 sheet: -1.21 (0.53), residues: 111 loop : -1.11 (0.42), 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 269 PHE 0.012 0.001 PHE A 294 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG F 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.97 seconds wall clock time: 59 minutes 39.62 seconds (3579.62 seconds total)