Starting phenix.real_space_refine on Sun Dec 29 23:34:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5f_27911/12_2024/8e5f_27911.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.032 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 Fe 20 7.16 5 S 70 5.16 5 C 7705 2.51 5 N 1920 2.21 5 O 2175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11890 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 19, 'TRANS': 273} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.53, per 1000 atoms: 0.47 Number of scatterers: 11890 At special positions: 0 Unit cell: (71.28, 75.6, 204.12, 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) Fe 20 26.01 S 70 16.00 O 2175 8.00 N 1920 7.00 C 7705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 20.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 78 through 84 removed outlier: 4.281A pdb=" N TRP A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.604A pdb=" N SER A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.513A pdb=" N SER A 287 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.541A pdb=" N TYR A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.659A pdb=" N PHE A 305 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 84 removed outlier: 4.281A pdb=" N TRP B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.604A pdb=" N SER B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.513A pdb=" N SER B 287 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.542A pdb=" N TYR B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.659A pdb=" N PHE B 305 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 4.281A pdb=" N TRP C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.604A pdb=" N SER C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.512A pdb=" N SER C 287 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.540A pdb=" N TYR C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.660A pdb=" N PHE C 305 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 removed outlier: 4.281A pdb=" N TRP D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.604A pdb=" N SER D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.513A pdb=" N SER D 287 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.541A pdb=" N TYR D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.660A pdb=" N PHE D 305 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 removed outlier: 4.281A pdb=" N TRP E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.604A pdb=" N SER E 110 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.513A pdb=" N SER E 287 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 293 removed outlier: 3.540A pdb=" N TYR E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.659A pdb=" N PHE E 305 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=2, first strand: chain 'A' and resid 172 through 176 removed outlier: 3.737A pdb=" N GLY A 166 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A 193 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=4, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=5, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.736A pdb=" N GLY B 166 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR B 193 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=7, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=8, first strand: chain 'C' and resid 172 through 176 removed outlier: 3.737A pdb=" N GLY C 166 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR C 193 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=10, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=11, first strand: chain 'D' and resid 172 through 176 removed outlier: 3.736A pdb=" N GLY D 166 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR D 193 " --> pdb=" O PHE D 277 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=13, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=14, first strand: chain 'E' and resid 172 through 176 removed outlier: 3.737A pdb=" N GLY E 166 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR E 193 " --> pdb=" O PHE E 277 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 201 through 203 260 hydrogen bonds defined for protein. 675 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: 3.01 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5340 1.39 - 1.56: 6860 1.56 - 1.73: 10 1.73 - 1.89: 80 1.89 - 2.06: 80 Bond restraints: 12370 Sorted by residual: bond pdb=" C2D HEC D 502 " pdb=" C3D HEC D 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC A 502 " pdb=" C3D HEC A 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC E 502 " pdb=" C3D HEC E 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 12365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 16937 3.31 - 6.63: 173 6.63 - 9.94: 25 9.94 - 13.26: 20 13.26 - 16.57: 35 Bond angle restraints: 17190 Sorted by residual: angle pdb=" CA PRO C 260 " pdb=" N PRO C 260 " pdb=" CD PRO C 260 " ideal model delta sigma weight residual 112.00 95.43 16.57 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO B 260 " pdb=" N PRO B 260 " pdb=" CD PRO B 260 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO D 260 " pdb=" N PRO D 260 " pdb=" CD PRO D 260 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO A 260 " pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 112.00 95.45 16.55 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO E 260 " pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 112.00 95.45 16.55 1.40e+00 5.10e-01 1.40e+02 ... (remaining 17185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6016 17.96 - 35.93: 495 35.93 - 53.89: 105 53.89 - 71.85: 45 71.85 - 89.82: 35 Dihedral angle restraints: 6696 sinusoidal: 2506 harmonic: 4190 Sorted by residual: dihedral pdb=" C2C HEC B 502 " pdb=" C3C HEC B 502 " pdb=" CAC HEC B 502 " pdb=" CBC HEC B 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.18 89.82 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2C HEC E 502 " pdb=" C3C HEC E 502 " pdb=" CAC HEC E 502 " pdb=" CBC HEC E 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.19 89.81 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2C HEC C 502 " pdb=" C3C HEC C 502 " pdb=" CAC HEC C 502 " pdb=" CBC HEC C 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.19 89.81 2 1.00e+01 1.00e-02 4.80e+01 ... (remaining 6693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1451 0.079 - 0.159: 219 0.159 - 0.238: 0 0.238 - 0.318: 10 0.318 - 0.397: 5 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA ARG D 234 " pdb=" N ARG D 234 " pdb=" C ARG D 234 " pdb=" CB ARG D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ARG E 234 " pdb=" N ARG E 234 " pdb=" C ARG E 234 " pdb=" CB ARG E 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA ARG A 234 " pdb=" N ARG A 234 " pdb=" C ARG A 234 " pdb=" CB ARG A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 1682 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 259 " 0.072 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO D 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 260 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 259 " 0.072 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 259 " 0.072 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO E 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " 0.052 5.00e-02 4.00e+02 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 142 2.60 - 3.18: 10264 3.18 - 3.75: 18218 3.75 - 4.33: 24735 4.33 - 4.90: 41815 Nonbonded interactions: 95174 Sorted by model distance: nonbonded pdb=" SG CYS C 62 " pdb=" SG CYS C 69 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 62 " pdb=" SG CYS E 69 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 62 " pdb=" SG CYS D 69 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 62 " pdb=" SG CYS B 69 " model vdw 2.029 3.760 nonbonded pdb=" NE2 HIS C 89 " pdb="FE HEC C 502 " model vdw 2.029 3.080 ... (remaining 95169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 26.860 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.017 0.249 12370 Z= 1.037 Angle : 1.167 16.575 17190 Z= 0.561 Chirality : 0.057 0.397 1685 Planarity : 0.006 0.097 2145 Dihedral : 16.511 89.819 4050 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 0.00 % Allowed : 15.74 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.21), residues: 1455 helix: -0.28 (0.37), residues: 210 sheet: -1.73 (0.47), residues: 150 loop : -2.56 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 93 HIS 0.004 0.001 HIS E 38 PHE 0.015 0.001 PHE C 309 TYR 0.010 0.001 TYR C 123 ARG 0.006 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.259 Fit side-chains REVERT: A 102 ASN cc_start: 0.8307 (t160) cc_final: 0.7910 (t0) REVERT: A 267 MET cc_start: 0.8940 (tpp) cc_final: 0.8359 (tpt) REVERT: B 102 ASN cc_start: 0.8395 (t160) cc_final: 0.8056 (t0) REVERT: C 102 ASN cc_start: 0.8318 (t160) cc_final: 0.8010 (t0) REVERT: D 102 ASN cc_start: 0.8348 (t160) cc_final: 0.7961 (t0) REVERT: D 156 ASP cc_start: 0.7953 (p0) cc_final: 0.7123 (p0) REVERT: E 260 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7874 (Cg_endo) REVERT: E 264 THR cc_start: 0.9126 (p) cc_final: 0.8906 (t) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2305 time to fit residues: 50.3234 Evaluate side-chains 130 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 229 GLN D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12370 Z= 0.286 Angle : 0.846 12.346 17190 Z= 0.373 Chirality : 0.050 0.215 1685 Planarity : 0.005 0.040 2145 Dihedral : 13.116 85.183 1735 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer: Outliers : 3.66 % Allowed : 12.85 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1455 helix: -0.34 (0.36), residues: 215 sheet: -2.31 (0.44), residues: 145 loop : -2.66 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 82 HIS 0.006 0.001 HIS D 273 PHE 0.016 0.002 PHE C 309 TYR 0.013 0.002 TYR B 283 ARG 0.005 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.169 Fit side-chains REVERT: A 102 ASN cc_start: 0.8442 (t160) cc_final: 0.7884 (t0) REVERT: A 130 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: A 156 ASP cc_start: 0.7765 (p0) cc_final: 0.6954 (p0) REVERT: A 267 MET cc_start: 0.8851 (tpp) cc_final: 0.8287 (tpt) REVERT: B 108 LEU cc_start: 0.8937 (tt) cc_final: 0.8724 (tp) REVERT: B 130 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 149 PHE cc_start: 0.9168 (p90) cc_final: 0.8932 (p90) REVERT: B 156 ASP cc_start: 0.7686 (p0) cc_final: 0.6861 (p0) REVERT: B 229 GLN cc_start: 0.8540 (pt0) cc_final: 0.8275 (pt0) REVERT: B 260 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7850 (Cg_endo) REVERT: C 102 ASN cc_start: 0.8435 (t160) cc_final: 0.7961 (t0) REVERT: C 130 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: D 102 ASN cc_start: 0.8479 (t160) cc_final: 0.8082 (t0) REVERT: D 130 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: D 156 ASP cc_start: 0.8008 (p0) cc_final: 0.7410 (p0) REVERT: D 260 PRO cc_start: 0.8016 (Cg_endo) cc_final: 0.7751 (Cg_endo) REVERT: E 102 ASN cc_start: 0.8440 (t160) cc_final: 0.8030 (t0) REVERT: E 130 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: E 264 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8758 (t) outliers start: 43 outliers final: 21 residues processed: 199 average time/residue: 0.2240 time to fit residues: 65.7338 Evaluate side-chains 174 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 0.0070 chunk 142 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12370 Z= 0.275 Angle : 0.813 13.856 17190 Z= 0.363 Chirality : 0.052 0.226 1685 Planarity : 0.004 0.042 2145 Dihedral : 13.075 86.492 1735 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.26 % Favored : 84.74 % Rotamer: Outliers : 3.23 % Allowed : 16.17 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.20), residues: 1455 helix: -0.20 (0.38), residues: 215 sheet: -2.29 (0.43), residues: 145 loop : -2.68 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 82 HIS 0.005 0.001 HIS E 273 PHE 0.012 0.002 PHE B 309 TYR 0.012 0.001 TYR A 283 ARG 0.004 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.268 Fit side-chains REVERT: A 102 ASN cc_start: 0.8516 (t160) cc_final: 0.7897 (t0) REVERT: A 130 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 156 ASP cc_start: 0.7761 (p0) cc_final: 0.6939 (p0) REVERT: A 187 GLU cc_start: 0.8880 (tp30) cc_final: 0.8281 (mm-30) REVERT: B 70 VAL cc_start: 0.8875 (p) cc_final: 0.8614 (m) REVERT: B 130 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7816 (m-10) REVERT: B 149 PHE cc_start: 0.9179 (p90) cc_final: 0.8912 (p90) REVERT: B 156 ASP cc_start: 0.7632 (p0) cc_final: 0.6888 (p0) REVERT: B 260 PRO cc_start: 0.8118 (Cg_endo) cc_final: 0.7908 (Cg_endo) REVERT: C 102 ASN cc_start: 0.8483 (t160) cc_final: 0.7958 (t0) REVERT: C 130 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: C 184 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8166 (mm-40) REVERT: C 187 GLU cc_start: 0.8814 (tp30) cc_final: 0.8399 (mm-30) REVERT: D 102 ASN cc_start: 0.8509 (t160) cc_final: 0.8013 (t0) REVERT: D 130 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8095 (m-10) REVERT: D 156 ASP cc_start: 0.8063 (p0) cc_final: 0.7381 (p0) REVERT: D 187 GLU cc_start: 0.8701 (tp30) cc_final: 0.8380 (mm-30) REVERT: D 288 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: E 66 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8141 (mm-40) REVERT: E 102 ASN cc_start: 0.8557 (t160) cc_final: 0.8074 (t0) REVERT: E 130 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: E 264 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8711 (t) outliers start: 38 outliers final: 24 residues processed: 181 average time/residue: 0.2097 time to fit residues: 58.1251 Evaluate side-chains 167 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 102 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12370 Z= 0.239 Angle : 0.763 11.879 17190 Z= 0.345 Chirality : 0.050 0.231 1685 Planarity : 0.004 0.038 2145 Dihedral : 12.958 85.542 1735 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 2.81 % Allowed : 17.53 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.20), residues: 1455 helix: -0.09 (0.38), residues: 215 sheet: -1.71 (0.46), residues: 150 loop : -2.74 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 82 HIS 0.004 0.001 HIS E 273 PHE 0.014 0.001 PHE A 224 TYR 0.011 0.001 TYR E 292 ARG 0.004 0.000 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.160 Fit side-chains REVERT: A 51 SER cc_start: 0.9176 (t) cc_final: 0.8891 (m) REVERT: A 66 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 102 ASN cc_start: 0.8469 (t160) cc_final: 0.7838 (t0) REVERT: A 130 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: A 156 ASP cc_start: 0.7637 (p0) cc_final: 0.6819 (p0) REVERT: B 70 VAL cc_start: 0.8866 (p) cc_final: 0.8634 (m) REVERT: B 130 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7805 (m-10) REVERT: B 149 PHE cc_start: 0.9133 (p90) cc_final: 0.8863 (p90) REVERT: B 156 ASP cc_start: 0.7504 (p0) cc_final: 0.6830 (p0) REVERT: B 299 PRO cc_start: 0.9349 (Cg_endo) cc_final: 0.8996 (Cg_exo) REVERT: C 130 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: C 187 GLU cc_start: 0.8769 (tp30) cc_final: 0.8145 (mm-30) REVERT: D 102 ASN cc_start: 0.8402 (t0) cc_final: 0.7847 (t0) REVERT: D 130 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: D 156 ASP cc_start: 0.7869 (p0) cc_final: 0.7204 (p0) REVERT: E 130 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: E 187 GLU cc_start: 0.8849 (tp30) cc_final: 0.8346 (mm-30) REVERT: E 264 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8669 (t) outliers start: 33 outliers final: 20 residues processed: 179 average time/residue: 0.1994 time to fit residues: 55.2228 Evaluate side-chains 165 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 102 ASN A 229 GLN B 74 GLN B 125 ASN C 74 GLN C 125 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 12370 Z= 0.611 Angle : 1.008 17.635 17190 Z= 0.452 Chirality : 0.058 0.276 1685 Planarity : 0.005 0.048 2145 Dihedral : 13.455 87.261 1735 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 4.94 % Allowed : 16.68 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.21), residues: 1455 helix: 0.03 (0.40), residues: 185 sheet: -1.76 (0.39), residues: 185 loop : -2.80 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 71 HIS 0.006 0.002 HIS B 89 PHE 0.024 0.003 PHE B 224 TYR 0.029 0.002 TYR E 123 ARG 0.004 0.001 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 1.241 Fit side-chains REVERT: A 130 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: A 280 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7822 (m) REVERT: B 69 CYS cc_start: 0.8905 (p) cc_final: 0.8302 (m) REVERT: B 70 VAL cc_start: 0.9127 (p) cc_final: 0.8841 (m) REVERT: B 130 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: B 156 ASP cc_start: 0.7871 (p0) cc_final: 0.7431 (p0) REVERT: C 130 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: C 280 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7758 (m) REVERT: D 66 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8501 (mm-40) REVERT: D 130 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: D 280 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7950 (m) REVERT: E 130 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: E 280 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7807 (m) outliers start: 58 outliers final: 35 residues processed: 175 average time/residue: 0.1879 time to fit residues: 52.0099 Evaluate side-chains 163 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 125 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12370 Z= 0.254 Angle : 0.833 13.910 17190 Z= 0.369 Chirality : 0.051 0.241 1685 Planarity : 0.004 0.042 2145 Dihedral : 13.094 89.202 1735 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 3.83 % Allowed : 18.64 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.20), residues: 1455 helix: -0.30 (0.38), residues: 205 sheet: -2.18 (0.43), residues: 145 loop : -2.90 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 82 HIS 0.006 0.001 HIS D 89 PHE 0.014 0.001 PHE E 224 TYR 0.030 0.002 TYR B 123 ARG 0.004 0.000 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.264 Fit side-chains REVERT: A 130 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: A 187 GLU cc_start: 0.8972 (tp30) cc_final: 0.8263 (mm-30) REVERT: A 280 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7361 (m) REVERT: B 70 VAL cc_start: 0.9111 (p) cc_final: 0.8855 (m) REVERT: B 130 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8003 (m-10) REVERT: B 280 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7569 (m) REVERT: B 299 PRO cc_start: 0.9384 (Cg_endo) cc_final: 0.9023 (Cg_exo) REVERT: C 130 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: C 280 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7357 (m) REVERT: D 66 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8468 (mm-40) REVERT: D 102 ASN cc_start: 0.8624 (t0) cc_final: 0.8093 (t0) REVERT: D 130 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: D 140 ARG cc_start: 0.8265 (tpm170) cc_final: 0.7986 (tpm170) REVERT: D 187 GLU cc_start: 0.8676 (tp30) cc_final: 0.8364 (mm-30) REVERT: D 280 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7588 (m) REVERT: E 130 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: E 280 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7309 (m) outliers start: 45 outliers final: 25 residues processed: 173 average time/residue: 0.1879 time to fit residues: 51.1676 Evaluate side-chains 155 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12370 Z= 0.280 Angle : 0.816 13.028 17190 Z= 0.362 Chirality : 0.051 0.262 1685 Planarity : 0.004 0.042 2145 Dihedral : 13.020 88.904 1735 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.19 % Favored : 84.81 % Rotamer: Outliers : 3.83 % Allowed : 19.49 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), residues: 1455 helix: -0.32 (0.38), residues: 205 sheet: -2.11 (0.44), residues: 145 loop : -2.92 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 82 HIS 0.004 0.001 HIS E 30 PHE 0.012 0.001 PHE D 309 TYR 0.026 0.001 TYR B 123 ARG 0.003 0.000 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.316 Fit side-chains REVERT: A 66 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8391 (mm-40) REVERT: A 130 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: A 280 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7363 (m) REVERT: B 70 VAL cc_start: 0.9158 (p) cc_final: 0.8921 (m) REVERT: B 102 ASN cc_start: 0.8528 (t0) cc_final: 0.8112 (t0) REVERT: B 130 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: B 156 ASP cc_start: 0.7862 (p0) cc_final: 0.7052 (p0) REVERT: B 183 MET cc_start: 0.8199 (mmp) cc_final: 0.7982 (mmp) REVERT: B 280 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7428 (m) REVERT: B 299 PRO cc_start: 0.9387 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: C 69 CYS cc_start: 0.8937 (p) cc_final: 0.8619 (m) REVERT: C 102 ASN cc_start: 0.8586 (t0) cc_final: 0.8082 (t0) REVERT: C 130 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: C 267 MET cc_start: 0.8519 (ttm) cc_final: 0.8285 (tpt) REVERT: C 280 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7373 (m) REVERT: D 102 ASN cc_start: 0.8585 (t0) cc_final: 0.7983 (t0) REVERT: D 130 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8111 (m-10) REVERT: D 140 ARG cc_start: 0.8326 (tpm170) cc_final: 0.8017 (tpm170) REVERT: D 280 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7427 (m) REVERT: E 130 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8103 (m-10) outliers start: 45 outliers final: 30 residues processed: 171 average time/residue: 0.2306 time to fit residues: 61.6193 Evaluate side-chains 166 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12370 Z= 0.264 Angle : 0.807 12.106 17190 Z= 0.360 Chirality : 0.050 0.279 1685 Planarity : 0.004 0.040 2145 Dihedral : 12.903 87.581 1735 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer: Outliers : 3.57 % Allowed : 20.09 % Favored : 76.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.20), residues: 1455 helix: -0.16 (0.38), residues: 215 sheet: -2.02 (0.44), residues: 145 loop : -2.91 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 89 PHE 0.011 0.001 PHE E 224 TYR 0.021 0.001 TYR E 123 ARG 0.003 0.000 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.349 Fit side-chains REVERT: A 66 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8340 (mm-40) REVERT: A 102 ASN cc_start: 0.8558 (t0) cc_final: 0.8089 (t0) REVERT: A 130 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: A 280 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7348 (m) REVERT: A 299 PRO cc_start: 0.9414 (Cg_endo) cc_final: 0.9018 (Cg_exo) REVERT: B 70 VAL cc_start: 0.9149 (p) cc_final: 0.8902 (m) REVERT: B 102 ASN cc_start: 0.8545 (t0) cc_final: 0.8066 (t0) REVERT: B 130 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7968 (m-10) REVERT: B 149 PHE cc_start: 0.9161 (p90) cc_final: 0.8946 (p90) REVERT: B 280 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7398 (m) REVERT: B 299 PRO cc_start: 0.9364 (Cg_endo) cc_final: 0.9008 (Cg_exo) REVERT: C 69 CYS cc_start: 0.8874 (p) cc_final: 0.8593 (m) REVERT: C 102 ASN cc_start: 0.8532 (t0) cc_final: 0.8030 (t0) REVERT: C 118 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8397 (t) REVERT: C 130 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: C 267 MET cc_start: 0.8501 (ttm) cc_final: 0.8136 (tpt) REVERT: C 280 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7341 (m) REVERT: D 66 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8514 (mm-40) REVERT: D 102 ASN cc_start: 0.8529 (t0) cc_final: 0.7939 (t0) REVERT: D 130 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: D 140 ARG cc_start: 0.8309 (tpm170) cc_final: 0.8005 (tpm170) REVERT: D 187 GLU cc_start: 0.8626 (tp30) cc_final: 0.8342 (mm-30) REVERT: D 229 GLN cc_start: 0.9128 (pp30) cc_final: 0.8037 (pp30) REVERT: D 280 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7392 (m) REVERT: E 130 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: E 280 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7202 (m) outliers start: 42 outliers final: 29 residues processed: 183 average time/residue: 0.1881 time to fit residues: 54.1819 Evaluate side-chains 176 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12370 Z= 0.263 Angle : 0.795 11.767 17190 Z= 0.355 Chirality : 0.050 0.245 1685 Planarity : 0.004 0.040 2145 Dihedral : 12.871 87.716 1735 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer: Outliers : 3.66 % Allowed : 20.43 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.20), residues: 1455 helix: -0.16 (0.38), residues: 215 sheet: -1.95 (0.44), residues: 145 loop : -2.93 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 89 PHE 0.013 0.001 PHE D 224 TYR 0.021 0.001 TYR E 123 ARG 0.003 0.000 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.273 Fit side-chains REVERT: A 66 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8350 (mm-40) REVERT: A 102 ASN cc_start: 0.8504 (t0) cc_final: 0.8042 (t0) REVERT: A 130 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 299 PRO cc_start: 0.9402 (Cg_endo) cc_final: 0.8984 (Cg_exo) REVERT: B 102 ASN cc_start: 0.8536 (t0) cc_final: 0.8017 (t0) REVERT: B 130 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: B 149 PHE cc_start: 0.9164 (p90) cc_final: 0.8959 (p90) REVERT: B 280 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7329 (m) REVERT: B 299 PRO cc_start: 0.9361 (Cg_endo) cc_final: 0.9000 (Cg_exo) REVERT: C 102 ASN cc_start: 0.8488 (t0) cc_final: 0.7976 (t0) REVERT: C 118 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8380 (t) REVERT: C 130 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: C 267 MET cc_start: 0.8496 (ttm) cc_final: 0.8135 (tpt) REVERT: C 280 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7270 (m) REVERT: D 102 ASN cc_start: 0.8480 (t0) cc_final: 0.7904 (t0) REVERT: D 130 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: D 140 ARG cc_start: 0.8294 (tpm170) cc_final: 0.7989 (tpm170) REVERT: D 187 GLU cc_start: 0.8646 (tp30) cc_final: 0.8347 (mm-30) REVERT: D 229 GLN cc_start: 0.9135 (pp30) cc_final: 0.8066 (pp30) REVERT: D 280 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7366 (m) REVERT: E 102 ASN cc_start: 0.8600 (t0) cc_final: 0.8048 (t0) REVERT: E 130 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7931 (m-10) REVERT: E 264 THR cc_start: 0.9121 (p) cc_final: 0.8784 (t) REVERT: E 280 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7141 (m) outliers start: 43 outliers final: 28 residues processed: 181 average time/residue: 0.1903 time to fit residues: 54.2081 Evaluate side-chains 179 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 48 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12370 Z= 0.309 Angle : 0.820 12.587 17190 Z= 0.365 Chirality : 0.051 0.260 1685 Planarity : 0.004 0.041 2145 Dihedral : 12.942 89.927 1735 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 3.57 % Allowed : 20.51 % Favored : 75.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.20), residues: 1455 helix: -0.16 (0.38), residues: 215 sheet: -1.95 (0.43), residues: 145 loop : -2.94 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.005 0.001 HIS D 89 PHE 0.013 0.001 PHE D 224 TYR 0.016 0.001 TYR D 123 ARG 0.003 0.000 ARG D 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.171 Fit side-chains REVERT: A 66 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8364 (mm-40) REVERT: A 102 ASN cc_start: 0.8547 (t0) cc_final: 0.8083 (t0) REVERT: A 130 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: A 280 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (m) REVERT: B 102 ASN cc_start: 0.8563 (t0) cc_final: 0.8082 (t0) REVERT: B 130 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: B 280 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7401 (m) REVERT: B 299 PRO cc_start: 0.9381 (Cg_endo) cc_final: 0.9025 (Cg_exo) REVERT: C 102 ASN cc_start: 0.8524 (t0) cc_final: 0.7991 (t0) REVERT: C 118 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8414 (t) REVERT: C 130 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: C 267 MET cc_start: 0.8519 (ttm) cc_final: 0.8123 (tpt) REVERT: C 280 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7419 (m) REVERT: D 102 ASN cc_start: 0.8507 (t0) cc_final: 0.7920 (t0) REVERT: D 130 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: D 140 ARG cc_start: 0.8351 (tpm170) cc_final: 0.8042 (tpm170) REVERT: D 229 GLN cc_start: 0.9142 (pp30) cc_final: 0.8086 (pp30) REVERT: D 280 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7497 (m) REVERT: E 102 ASN cc_start: 0.8626 (t0) cc_final: 0.7981 (t0) REVERT: E 130 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: E 264 THR cc_start: 0.9147 (p) cc_final: 0.8814 (t) REVERT: E 280 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7295 (m) outliers start: 42 outliers final: 29 residues processed: 177 average time/residue: 0.1930 time to fit residues: 53.7296 Evaluate side-chains 180 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088140 restraints weight = 22993.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090877 restraints weight = 11496.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.092671 restraints weight = 7147.791| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 12370 Z= 0.452 Angle : 0.917 14.606 17190 Z= 0.409 Chirality : 0.054 0.249 1685 Planarity : 0.005 0.045 2145 Dihedral : 13.219 89.656 1735 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.43 % Favored : 83.57 % Rotamer: Outliers : 3.83 % Allowed : 20.43 % Favored : 75.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.20), residues: 1455 helix: -0.30 (0.38), residues: 215 sheet: -2.08 (0.43), residues: 145 loop : -2.98 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.007 0.002 HIS B 89 PHE 0.018 0.002 PHE D 224 TYR 0.035 0.002 TYR D 123 ARG 0.003 0.001 ARG D 288 =============================================================================== Job complete usr+sys time: 2184.65 seconds wall clock time: 41 minutes 44.08 seconds (2504.08 seconds total)