Starting phenix.real_space_refine on Wed Sep 25 01:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/09_2024/6d7l_7823.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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5760 2.51 5 N 1584 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Restraints were copied for chains: C, B, D Time building chain proxies: 4.66, per 1000 atoms: 0.51 Number of scatterers: 9172 At special positions: 0 Unit cell: (108.504, 108.504, 78.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1772 8.00 N 1584 7.00 C 5760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 69.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.847A pdb=" N TYR A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.604A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.537A pdb=" N VAL A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'A' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 796 Processing helix chain 'B' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.847A pdb=" N TYR C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.860A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.536A pdb=" N VAL C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 182 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 796 Processing helix chain 'C' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU C 804 " --> pdb=" O ASN C 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.827A pdb=" N HIS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.566A pdb=" N THR D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 796 Processing helix chain 'D' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU D 804 " --> pdb=" O ASN D 800 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1503 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: 2.17 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3084 1.34 - 1.46: 1532 1.46 - 1.58: 4588 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9288 Sorted by residual: bond pdb=" C SER A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER C 158 " pdb=" N PRO C 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER D 158 " pdb=" N PRO D 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER B 158 " pdb=" N PRO B 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 3.94e+00 bond pdb=" N PRO C 224 " pdb=" CD PRO C 224 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.44e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11848 1.72 - 3.45: 496 3.45 - 5.17: 100 5.17 - 6.89: 24 6.89 - 8.62: 12 Bond angle restraints: 12480 Sorted by residual: angle pdb=" C GLU B 232 " pdb=" N ASP B 233 " pdb=" CA ASP B 233 " ideal model delta sigma weight residual 122.83 127.55 -4.72 1.08e+00 8.57e-01 1.91e+01 angle pdb=" C GLU D 232 " pdb=" N ASP D 233 " pdb=" CA ASP D 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU A 232 " pdb=" N ASP A 233 " pdb=" CA ASP A 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU C 232 " pdb=" N ASP C 233 " pdb=" CA ASP C 233 " ideal model delta sigma weight residual 122.83 127.50 -4.67 1.08e+00 8.57e-01 1.87e+01 angle pdb=" N HIS D 124 " pdb=" CA HIS D 124 " pdb=" C HIS D 124 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.43: 5112 9.43 - 18.85: 644 18.85 - 28.28: 24 28.28 - 37.71: 12 37.71 - 47.14: 12 Dihedral angle restraints: 5804 sinusoidal: 2412 harmonic: 3392 Sorted by residual: dihedral pdb=" CA SER C 158 " pdb=" C SER C 158 " pdb=" N PRO C 159 " pdb=" CA PRO C 159 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER D 158 " pdb=" C SER D 158 " pdb=" N PRO D 159 " pdb=" CA PRO D 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 158 " pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 925 0.044 - 0.088: 382 0.088 - 0.132: 82 0.132 - 0.177: 25 0.177 - 0.221: 6 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA HIS C 124 " pdb=" N HIS C 124 " pdb=" C HIS C 124 " pdb=" CB HIS C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA HIS A 124 " pdb=" N HIS A 124 " pdb=" C HIS A 124 " pdb=" CB HIS A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS B 124 " pdb=" N HIS B 124 " pdb=" C HIS B 124 " pdb=" CB HIS B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1417 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 158 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 159 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 233 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO D 234 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 158 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.027 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2323 2.80 - 3.32: 8416 3.32 - 3.85: 13449 3.85 - 4.37: 16353 4.37 - 4.90: 26973 Nonbonded interactions: 67514 Sorted by model distance: nonbonded pdb=" O VAL C 82 " pdb=" OH TYR C 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL B 82 " pdb=" OH TYR B 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 82 " pdb=" OH TYR A 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL D 82 " pdb=" OH TYR D 114 " model vdw 2.273 3.040 nonbonded pdb=" NZ LYS A 808 " pdb=" OE1 GLU D 806 " model vdw 2.299 3.120 ... (remaining 67509 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' } 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: 0.940 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.004 0.064 9288 Z= 0.265 Angle : 0.861 8.617 12480 Z= 0.488 Chirality : 0.052 0.221 1420 Planarity : 0.005 0.048 1612 Dihedral : 7.646 47.136 3596 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.90 (0.18), residues: 1128 helix: -1.64 (0.14), residues: 780 sheet: None (None), residues: 0 loop : -4.70 (0.21), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 124 PHE 0.010 0.002 PHE A 193 TYR 0.014 0.002 TYR C 218 ARG 0.008 0.001 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.178 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 65 LEU cc_start: 0.7402 (mt) cc_final: 0.6838 (mp) REVERT: A 72 TYR cc_start: 0.6654 (m-80) cc_final: 0.5605 (m-80) REVERT: A 245 LEU cc_start: 0.9360 (mt) cc_final: 0.9144 (mt) REVERT: A 265 GLN cc_start: 0.9335 (mt0) cc_final: 0.9003 (mt0) REVERT: A 793 ASP cc_start: 0.8786 (m-30) cc_final: 0.8451 (t0) REVERT: A 822 LYS cc_start: 0.8562 (mttt) cc_final: 0.8319 (tppt) REVERT: B 65 LEU cc_start: 0.7305 (mt) cc_final: 0.6463 (mp) REVERT: B 72 TYR cc_start: 0.6631 (m-80) cc_final: 0.6130 (m-80) REVERT: B 245 LEU cc_start: 0.9361 (mt) cc_final: 0.9142 (mt) REVERT: B 265 GLN cc_start: 0.9336 (mt0) cc_final: 0.8992 (mt0) REVERT: B 793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8457 (t0) REVERT: C 65 LEU cc_start: 0.7303 (mt) cc_final: 0.6465 (mp) REVERT: C 72 TYR cc_start: 0.6668 (m-80) cc_final: 0.6067 (m-80) REVERT: C 245 LEU cc_start: 0.9382 (mt) cc_final: 0.9163 (mt) REVERT: C 265 GLN cc_start: 0.9345 (mt0) cc_final: 0.9014 (mt0) REVERT: C 793 ASP cc_start: 0.8782 (m-30) cc_final: 0.8428 (t0) REVERT: D 65 LEU cc_start: 0.7403 (mt) cc_final: 0.6835 (mp) REVERT: D 72 TYR cc_start: 0.6656 (m-80) cc_final: 0.6088 (m-80) REVERT: D 245 LEU cc_start: 0.9362 (mt) cc_final: 0.9143 (mt) REVERT: D 265 GLN cc_start: 0.9337 (mt0) cc_final: 0.9004 (mt0) REVERT: D 793 ASP cc_start: 0.8780 (m-30) cc_final: 0.8455 (t0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2818 time to fit residues: 148.7725 Evaluate side-chains 226 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS A 177 HIS B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 177 HIS C 66 ASN C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 177 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 177 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.216 Angle : 0.750 6.462 12480 Z= 0.384 Chirality : 0.043 0.128 1420 Planarity : 0.004 0.046 1612 Dihedral : 5.669 19.694 1248 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.25 % Allowed : 9.74 % Favored : 87.01 % 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: -2.09 (0.22), residues: 1128 helix: -0.02 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -4.76 (0.20), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 169 PHE 0.006 0.001 PHE A 43 TYR 0.013 0.001 TYR C 192 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 1.094 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: A 79 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8178 (pp30) REVERT: A 91 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8437 (mt-10) REVERT: A 174 GLU cc_start: 0.7047 (tp30) cc_final: 0.6569 (tp30) REVERT: A 245 LEU cc_start: 0.9402 (mt) cc_final: 0.9183 (mt) REVERT: A 265 GLN cc_start: 0.9323 (mt0) cc_final: 0.8994 (mt0) REVERT: A 793 ASP cc_start: 0.8771 (m-30) cc_final: 0.8516 (t0) REVERT: A 794 LYS cc_start: 0.9002 (tptp) cc_final: 0.8506 (tppp) REVERT: A 795 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8250 (mm-30) REVERT: A 817 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8658 (mt-10) REVERT: B 91 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 174 GLU cc_start: 0.7051 (tp30) cc_final: 0.6583 (tp30) REVERT: B 245 LEU cc_start: 0.9397 (mt) cc_final: 0.9167 (mt) REVERT: B 265 GLN cc_start: 0.9308 (mt0) cc_final: 0.8930 (mp10) REVERT: B 793 ASP cc_start: 0.8772 (m-30) cc_final: 0.8517 (t0) REVERT: B 794 LYS cc_start: 0.9000 (tptp) cc_final: 0.8506 (tppp) REVERT: B 795 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 819 LEU cc_start: 0.9146 (mt) cc_final: 0.8881 (pp) REVERT: C 91 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8421 (mt-10) REVERT: C 174 GLU cc_start: 0.7051 (tp30) cc_final: 0.6570 (tp30) REVERT: C 245 LEU cc_start: 0.9401 (mt) cc_final: 0.9184 (mt) REVERT: C 265 GLN cc_start: 0.9329 (mt0) cc_final: 0.8993 (mt0) REVERT: C 793 ASP cc_start: 0.8767 (m-30) cc_final: 0.8517 (t0) REVERT: C 794 LYS cc_start: 0.9006 (tptp) cc_final: 0.8508 (tppp) REVERT: C 795 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 91 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8448 (mt-10) REVERT: D 174 GLU cc_start: 0.7056 (tp30) cc_final: 0.6628 (tp30) REVERT: D 245 LEU cc_start: 0.9401 (mt) cc_final: 0.9183 (mt) REVERT: D 265 GLN cc_start: 0.9328 (mt0) cc_final: 0.8997 (mt0) REVERT: D 793 ASP cc_start: 0.8768 (m-30) cc_final: 0.8516 (t0) REVERT: D 794 LYS cc_start: 0.9005 (tptp) cc_final: 0.8514 (tppp) REVERT: D 795 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8236 (mm-30) REVERT: D 819 LEU cc_start: 0.9124 (mt) cc_final: 0.8906 (pp) outliers start: 33 outliers final: 12 residues processed: 265 average time/residue: 0.2338 time to fit residues: 82.4954 Evaluate side-chains 184 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.232 Angle : 0.798 14.428 12480 Z= 0.390 Chirality : 0.044 0.259 1420 Planarity : 0.005 0.058 1612 Dihedral : 5.410 19.299 1248 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.07 % Allowed : 12.40 % Favored : 85.53 % 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: -1.40 (0.24), residues: 1128 helix: 0.57 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -4.68 (0.19), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 169 PHE 0.005 0.001 PHE C 193 TYR 0.016 0.001 TYR A 49 ARG 0.010 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.7079 (p-80) REVERT: A 91 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8423 (mt-10) REVERT: A 174 GLU cc_start: 0.7096 (tp30) cc_final: 0.6538 (tp30) REVERT: A 264 MET cc_start: 0.8925 (mmm) cc_final: 0.8638 (mmm) REVERT: A 265 GLN cc_start: 0.9323 (mt0) cc_final: 0.8612 (mt0) REVERT: A 793 ASP cc_start: 0.8735 (m-30) cc_final: 0.8379 (t0) REVERT: A 795 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8304 (mm-30) REVERT: B 66 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8828 (p0) REVERT: B 86 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.7048 (p-80) REVERT: B 91 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 174 GLU cc_start: 0.7096 (tp30) cc_final: 0.6554 (tp30) REVERT: B 264 MET cc_start: 0.8934 (mmm) cc_final: 0.8713 (mmm) REVERT: B 265 GLN cc_start: 0.9325 (mt0) cc_final: 0.8662 (mp10) REVERT: B 793 ASP cc_start: 0.8735 (m-30) cc_final: 0.8384 (t0) REVERT: B 795 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8306 (mm-30) REVERT: B 819 LEU cc_start: 0.9132 (mt) cc_final: 0.8889 (pp) REVERT: C 86 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.7040 (p-80) REVERT: C 91 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8417 (mt-10) REVERT: C 174 GLU cc_start: 0.7087 (tp30) cc_final: 0.6557 (tp30) REVERT: C 264 MET cc_start: 0.8931 (mmm) cc_final: 0.8653 (mmm) REVERT: C 265 GLN cc_start: 0.9328 (mt0) cc_final: 0.8618 (mt0) REVERT: C 793 ASP cc_start: 0.8738 (m-30) cc_final: 0.8378 (t0) REVERT: C 795 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 86 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6975 (p-80) REVERT: D 91 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 174 GLU cc_start: 0.6982 (tp30) cc_final: 0.6549 (tp30) REVERT: D 178 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8018 (ptm) REVERT: D 264 MET cc_start: 0.8928 (mmm) cc_final: 0.8646 (mmm) REVERT: D 265 GLN cc_start: 0.9334 (mt0) cc_final: 0.8642 (mt0) REVERT: D 793 ASP cc_start: 0.8732 (m-30) cc_final: 0.8378 (t0) REVERT: D 795 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8309 (mm-30) outliers start: 21 outliers final: 9 residues processed: 207 average time/residue: 0.1838 time to fit residues: 54.4448 Evaluate side-chains 187 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.194 Angle : 0.759 11.518 12480 Z= 0.380 Chirality : 0.043 0.229 1420 Planarity : 0.005 0.070 1612 Dihedral : 5.208 18.726 1248 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.36 % Allowed : 12.70 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1128 helix: 0.87 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -4.55 (0.21), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 169 PHE 0.004 0.001 PHE C 193 TYR 0.015 0.001 TYR D 72 ARG 0.006 0.000 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.049 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: A 48 GLU cc_start: 0.8426 (tt0) cc_final: 0.7894 (tt0) REVERT: A 79 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8204 (pp30) REVERT: A 91 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 174 GLU cc_start: 0.7201 (tp30) cc_final: 0.6583 (tp30) REVERT: A 265 GLN cc_start: 0.9175 (mt0) cc_final: 0.8892 (mp10) REVERT: A 793 ASP cc_start: 0.8687 (m-30) cc_final: 0.8440 (t0) REVERT: A 794 LYS cc_start: 0.8943 (tptp) cc_final: 0.8468 (tppp) REVERT: B 91 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 174 GLU cc_start: 0.7197 (tp30) cc_final: 0.6528 (tp30) REVERT: B 265 GLN cc_start: 0.9181 (mt0) cc_final: 0.8899 (mp10) REVERT: B 793 ASP cc_start: 0.8691 (m-30) cc_final: 0.8447 (t0) REVERT: B 794 LYS cc_start: 0.8941 (tptp) cc_final: 0.8469 (tppp) REVERT: C 66 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (p0) REVERT: C 91 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8384 (mt-10) REVERT: C 174 GLU cc_start: 0.7199 (tp30) cc_final: 0.6517 (tp30) REVERT: C 265 GLN cc_start: 0.9180 (mt0) cc_final: 0.8897 (mp10) REVERT: C 793 ASP cc_start: 0.8686 (m-30) cc_final: 0.8439 (t0) REVERT: C 794 LYS cc_start: 0.8944 (tptp) cc_final: 0.8469 (tppp) REVERT: D 86 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6781 (p-80) REVERT: D 91 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8378 (mt-10) REVERT: D 174 GLU cc_start: 0.7068 (tp30) cc_final: 0.6530 (tp30) REVERT: D 265 GLN cc_start: 0.9182 (mt0) cc_final: 0.8897 (mp10) REVERT: D 793 ASP cc_start: 0.8689 (m-30) cc_final: 0.8441 (t0) REVERT: D 794 LYS cc_start: 0.8944 (tptp) cc_final: 0.8474 (tppp) REVERT: D 795 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8358 (mm-30) outliers start: 24 outliers final: 9 residues processed: 204 average time/residue: 0.1679 time to fit residues: 50.0537 Evaluate side-chains 176 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9288 Z= 0.204 Angle : 0.763 12.299 12480 Z= 0.379 Chirality : 0.044 0.215 1420 Planarity : 0.004 0.048 1612 Dihedral : 5.073 18.709 1248 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.48 % Allowed : 15.35 % Favored : 83.17 % 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: -0.75 (0.25), residues: 1128 helix: 1.06 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.40 (0.22), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 169 PHE 0.006 0.001 PHE C 193 TYR 0.015 0.001 TYR A 72 ARG 0.005 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.047 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: A 48 GLU cc_start: 0.8365 (tt0) cc_final: 0.7862 (tt0) REVERT: A 49 TYR cc_start: 0.8195 (m-10) cc_final: 0.7774 (m-10) REVERT: A 79 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8275 (pp30) REVERT: A 91 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8405 (mt-10) REVERT: A 174 GLU cc_start: 0.7083 (tp30) cc_final: 0.6729 (tp30) REVERT: A 265 GLN cc_start: 0.9156 (mt0) cc_final: 0.8876 (mp10) REVERT: A 793 ASP cc_start: 0.8701 (m-30) cc_final: 0.8473 (t0) REVERT: B 91 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 174 GLU cc_start: 0.7078 (tp30) cc_final: 0.6722 (tp30) REVERT: B 265 GLN cc_start: 0.9158 (mt0) cc_final: 0.8877 (mp10) REVERT: B 773 THR cc_start: 0.6415 (p) cc_final: 0.5902 (t) REVERT: B 793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8476 (t0) REVERT: C 91 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8420 (mt-10) REVERT: C 174 GLU cc_start: 0.7119 (tp30) cc_final: 0.6799 (tp30) REVERT: C 265 GLN cc_start: 0.9177 (mt0) cc_final: 0.8886 (mp10) REVERT: C 773 THR cc_start: 0.6411 (p) cc_final: 0.5896 (t) REVERT: C 793 ASP cc_start: 0.8725 (m-30) cc_final: 0.8472 (t0) REVERT: D 91 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 174 GLU cc_start: 0.7116 (tp30) cc_final: 0.6504 (tp30) REVERT: D 265 GLN cc_start: 0.9176 (mt0) cc_final: 0.8889 (mp10) REVERT: D 793 ASP cc_start: 0.8716 (m-30) cc_final: 0.8483 (t0) outliers start: 15 outliers final: 11 residues processed: 203 average time/residue: 0.1784 time to fit residues: 51.8766 Evaluate side-chains 174 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9288 Z= 0.216 Angle : 0.797 12.530 12480 Z= 0.397 Chirality : 0.043 0.198 1420 Planarity : 0.004 0.043 1612 Dihedral : 4.995 18.501 1248 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.85 % Allowed : 17.22 % Favored : 79.92 % 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: -0.61 (0.25), residues: 1128 helix: 1.17 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.41 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 169 PHE 0.004 0.001 PHE C 193 TYR 0.011 0.001 TYR C 72 ARG 0.005 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.144 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: A 48 GLU cc_start: 0.8438 (tt0) cc_final: 0.7772 (tt0) REVERT: A 49 TYR cc_start: 0.8190 (m-10) cc_final: 0.7604 (m-10) REVERT: A 79 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8239 (pp30) REVERT: A 91 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 174 GLU cc_start: 0.7154 (tp30) cc_final: 0.6756 (tp30) REVERT: A 265 GLN cc_start: 0.9187 (mt0) cc_final: 0.8887 (mp10) REVERT: A 793 ASP cc_start: 0.8709 (m-30) cc_final: 0.8457 (t0) REVERT: A 794 LYS cc_start: 0.8941 (tptp) cc_final: 0.8444 (tppp) REVERT: A 795 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: A 810 ASP cc_start: 0.8307 (p0) cc_final: 0.7778 (m-30) REVERT: B 91 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 174 GLU cc_start: 0.7138 (tp30) cc_final: 0.6782 (tp30) REVERT: B 265 GLN cc_start: 0.9185 (mt0) cc_final: 0.8883 (mp10) REVERT: B 793 ASP cc_start: 0.8710 (m-30) cc_final: 0.8459 (t0) REVERT: B 794 LYS cc_start: 0.8939 (tptp) cc_final: 0.8443 (tppp) REVERT: B 795 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: B 810 ASP cc_start: 0.8285 (p0) cc_final: 0.7852 (m-30) REVERT: C 91 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8316 (mt-10) REVERT: C 165 ILE cc_start: 0.9428 (mm) cc_final: 0.8929 (tt) REVERT: C 174 GLU cc_start: 0.7147 (tp30) cc_final: 0.6826 (tp30) REVERT: C 265 GLN cc_start: 0.9188 (mt0) cc_final: 0.8885 (mp10) REVERT: C 793 ASP cc_start: 0.8703 (m-30) cc_final: 0.8457 (t0) REVERT: C 794 LYS cc_start: 0.8940 (tptp) cc_final: 0.8443 (tppp) REVERT: C 795 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: C 810 ASP cc_start: 0.8290 (p0) cc_final: 0.7741 (m-30) REVERT: D 91 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8297 (mt-10) REVERT: D 174 GLU cc_start: 0.7172 (tp30) cc_final: 0.6782 (tp30) REVERT: D 265 GLN cc_start: 0.9191 (mt0) cc_final: 0.8886 (mp10) REVERT: D 793 ASP cc_start: 0.8732 (m-30) cc_final: 0.8461 (t0) REVERT: D 794 LYS cc_start: 0.8936 (tptp) cc_final: 0.8464 (tppp) REVERT: D 810 ASP cc_start: 0.8281 (p0) cc_final: 0.7848 (m-30) outliers start: 29 outliers final: 14 residues processed: 189 average time/residue: 0.1724 time to fit residues: 47.4244 Evaluate side-chains 173 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 795 GLU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9288 Z= 0.203 Angle : 0.806 13.152 12480 Z= 0.394 Chirality : 0.046 0.311 1420 Planarity : 0.004 0.036 1612 Dihedral : 4.931 17.913 1248 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.74 % Allowed : 16.24 % Favored : 80.02 % 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: -0.55 (0.25), residues: 1128 helix: 1.22 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.40 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 169 PHE 0.008 0.001 PHE C 193 TYR 0.018 0.001 TYR A 72 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.195 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: A 48 GLU cc_start: 0.8427 (tt0) cc_final: 0.7893 (tt0) REVERT: A 49 TYR cc_start: 0.8131 (m-10) cc_final: 0.7581 (m-10) REVERT: A 91 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 174 GLU cc_start: 0.7155 (tp30) cc_final: 0.6759 (tp30) REVERT: A 265 GLN cc_start: 0.9198 (mt0) cc_final: 0.8919 (mp10) REVERT: A 793 ASP cc_start: 0.8693 (m-30) cc_final: 0.8440 (t0) REVERT: A 794 LYS cc_start: 0.8905 (tptp) cc_final: 0.8453 (tppp) REVERT: B 91 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 174 GLU cc_start: 0.7152 (tp30) cc_final: 0.6723 (tp30) REVERT: B 265 GLN cc_start: 0.9194 (mt0) cc_final: 0.8916 (mp10) REVERT: B 793 ASP cc_start: 0.8693 (m-30) cc_final: 0.8442 (t0) REVERT: B 794 LYS cc_start: 0.8903 (tptp) cc_final: 0.8449 (tppp) REVERT: B 795 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8396 (mm-30) REVERT: B 810 ASP cc_start: 0.8287 (p0) cc_final: 0.7889 (m-30) REVERT: C 91 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 165 ILE cc_start: 0.9436 (mm) cc_final: 0.8927 (tt) REVERT: C 174 GLU cc_start: 0.7282 (tp30) cc_final: 0.6766 (tp30) REVERT: C 265 GLN cc_start: 0.9202 (mt0) cc_final: 0.8925 (mp10) REVERT: C 793 ASP cc_start: 0.8692 (m-30) cc_final: 0.8442 (t0) REVERT: C 794 LYS cc_start: 0.8906 (tptp) cc_final: 0.8452 (tppp) REVERT: C 810 ASP cc_start: 0.8335 (p0) cc_final: 0.8055 (p0) REVERT: D 91 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 174 GLU cc_start: 0.7168 (tp30) cc_final: 0.6749 (tp30) REVERT: D 265 GLN cc_start: 0.9203 (mt0) cc_final: 0.8927 (mp10) REVERT: D 793 ASP cc_start: 0.8717 (m-30) cc_final: 0.8464 (t0) REVERT: D 794 LYS cc_start: 0.8899 (tptp) cc_final: 0.8455 (tppp) REVERT: D 810 ASP cc_start: 0.8291 (p0) cc_final: 0.7900 (m-30) outliers start: 38 outliers final: 16 residues processed: 198 average time/residue: 0.1699 time to fit residues: 49.3856 Evaluate side-chains 171 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9288 Z= 0.210 Angle : 0.839 13.260 12480 Z= 0.416 Chirality : 0.047 0.317 1420 Planarity : 0.004 0.034 1612 Dihedral : 4.868 17.386 1248 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.97 % Allowed : 18.70 % Favored : 79.33 % 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: -0.51 (0.25), residues: 1128 helix: 1.25 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.39 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 124 PHE 0.003 0.001 PHE C 193 TYR 0.010 0.001 TYR C 72 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8471 (tt0) cc_final: 0.7681 (tt0) REVERT: A 49 TYR cc_start: 0.8141 (m-10) cc_final: 0.7380 (m-80) REVERT: A 79 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7971 (pp30) REVERT: A 174 GLU cc_start: 0.7195 (tp30) cc_final: 0.6508 (tp30) REVERT: A 265 GLN cc_start: 0.9202 (mt0) cc_final: 0.8923 (mp10) REVERT: A 793 ASP cc_start: 0.8703 (m-30) cc_final: 0.8449 (t0) REVERT: A 794 LYS cc_start: 0.8878 (tptp) cc_final: 0.8451 (tppp) REVERT: B 91 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8325 (mt-10) REVERT: B 174 GLU cc_start: 0.7205 (tp30) cc_final: 0.6509 (tp30) REVERT: B 265 GLN cc_start: 0.9199 (mt0) cc_final: 0.8918 (mp10) REVERT: B 793 ASP cc_start: 0.8699 (m-30) cc_final: 0.8459 (t0) REVERT: B 794 LYS cc_start: 0.8883 (tptp) cc_final: 0.8463 (tppp) REVERT: B 810 ASP cc_start: 0.8314 (p0) cc_final: 0.8006 (m-30) REVERT: C 165 ILE cc_start: 0.9448 (mm) cc_final: 0.8942 (tt) REVERT: C 174 GLU cc_start: 0.7313 (tp30) cc_final: 0.6554 (tp30) REVERT: C 265 GLN cc_start: 0.9206 (mt0) cc_final: 0.8923 (mp10) REVERT: C 793 ASP cc_start: 0.8699 (m-30) cc_final: 0.8449 (t0) REVERT: C 794 LYS cc_start: 0.8883 (tptp) cc_final: 0.8456 (tppp) REVERT: D 91 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8315 (mt-10) REVERT: D 174 GLU cc_start: 0.7055 (tp30) cc_final: 0.6849 (tp30) REVERT: D 265 GLN cc_start: 0.9207 (mt0) cc_final: 0.8924 (mp10) REVERT: D 793 ASP cc_start: 0.8704 (m-30) cc_final: 0.8448 (t0) REVERT: D 794 LYS cc_start: 0.8870 (tptp) cc_final: 0.8447 (tppp) REVERT: D 810 ASP cc_start: 0.8309 (p0) cc_final: 0.8016 (m-30) outliers start: 20 outliers final: 17 residues processed: 184 average time/residue: 0.1810 time to fit residues: 47.7667 Evaluate side-chains 169 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0870 chunk 100 optimal weight: 0.0040 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 106 optimal weight: 5.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9288 Z= 0.215 Angle : 0.869 13.373 12480 Z= 0.425 Chirality : 0.047 0.339 1420 Planarity : 0.004 0.031 1612 Dihedral : 4.829 16.983 1248 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.97 % Allowed : 20.37 % Favored : 77.66 % 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: -0.57 (0.25), residues: 1128 helix: 1.22 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.46 (0.21), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 169 PHE 0.007 0.001 PHE C 193 TYR 0.019 0.001 TYR A 72 ARG 0.008 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8513 (tt0) cc_final: 0.7740 (tt0) REVERT: A 49 TYR cc_start: 0.8146 (m-10) cc_final: 0.7504 (m-80) REVERT: A 79 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7956 (pp30) REVERT: A 174 GLU cc_start: 0.7153 (tp30) cc_final: 0.6768 (tp30) REVERT: A 265 GLN cc_start: 0.9190 (mt0) cc_final: 0.8916 (mp10) REVERT: A 793 ASP cc_start: 0.8666 (m-30) cc_final: 0.8431 (t0) REVERT: A 794 LYS cc_start: 0.8837 (tptp) cc_final: 0.8425 (tppp) REVERT: B 174 GLU cc_start: 0.7132 (tp30) cc_final: 0.6778 (tp30) REVERT: B 265 GLN cc_start: 0.9186 (mt0) cc_final: 0.8910 (mp10) REVERT: B 793 ASP cc_start: 0.8667 (m-30) cc_final: 0.8429 (t0) REVERT: B 794 LYS cc_start: 0.8862 (tptp) cc_final: 0.8452 (tppp) REVERT: B 810 ASP cc_start: 0.8294 (p0) cc_final: 0.7985 (m-30) REVERT: C 165 ILE cc_start: 0.9444 (mm) cc_final: 0.8942 (tt) REVERT: C 174 GLU cc_start: 0.7217 (tp30) cc_final: 0.6775 (tp30) REVERT: C 265 GLN cc_start: 0.9193 (mt0) cc_final: 0.8915 (mp10) REVERT: C 793 ASP cc_start: 0.8664 (m-30) cc_final: 0.8414 (t0) REVERT: C 794 LYS cc_start: 0.8842 (tptp) cc_final: 0.8434 (tppp) REVERT: D 174 GLU cc_start: 0.7181 (tp30) cc_final: 0.6853 (tp30) REVERT: D 265 GLN cc_start: 0.9194 (mt0) cc_final: 0.8917 (mp10) REVERT: D 793 ASP cc_start: 0.8669 (m-30) cc_final: 0.8440 (t0) REVERT: D 794 LYS cc_start: 0.8856 (tptp) cc_final: 0.8442 (tppp) REVERT: D 810 ASP cc_start: 0.8283 (p0) cc_final: 0.7976 (m-30) outliers start: 20 outliers final: 16 residues processed: 186 average time/residue: 0.1862 time to fit residues: 49.7361 Evaluate side-chains 169 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9288 Z= 0.227 Angle : 0.915 13.488 12480 Z= 0.444 Chirality : 0.050 0.340 1420 Planarity : 0.004 0.032 1612 Dihedral : 4.787 16.601 1248 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.77 % Allowed : 21.36 % Favored : 76.87 % 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: -0.71 (0.25), residues: 1128 helix: 1.10 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.44 (0.21), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 169 PHE 0.009 0.001 PHE A 269 TYR 0.012 0.001 TYR C 72 ARG 0.009 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.019 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: A 48 GLU cc_start: 0.8496 (tt0) cc_final: 0.7800 (tt0) REVERT: A 49 TYR cc_start: 0.8059 (m-10) cc_final: 0.7763 (m-10) REVERT: A 79 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7868 (pp30) REVERT: A 91 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 174 GLU cc_start: 0.7109 (tp30) cc_final: 0.6744 (tp30) REVERT: A 265 GLN cc_start: 0.9131 (mt0) cc_final: 0.8873 (mp10) REVERT: A 793 ASP cc_start: 0.8664 (m-30) cc_final: 0.8430 (t0) REVERT: A 794 LYS cc_start: 0.8860 (tptp) cc_final: 0.8455 (tppp) REVERT: B 174 GLU cc_start: 0.7106 (tp30) cc_final: 0.6735 (tp30) REVERT: B 265 GLN cc_start: 0.9116 (mt0) cc_final: 0.8840 (mp10) REVERT: B 793 ASP cc_start: 0.8639 (m-30) cc_final: 0.8399 (t0) REVERT: B 794 LYS cc_start: 0.8888 (tptp) cc_final: 0.8338 (tppp) REVERT: B 795 GLU cc_start: 0.8529 (mp0) cc_final: 0.7983 (mp0) REVERT: B 810 ASP cc_start: 0.8259 (p0) cc_final: 0.7950 (m-30) REVERT: C 165 ILE cc_start: 0.9451 (mm) cc_final: 0.8934 (tt) REVERT: C 174 GLU cc_start: 0.7185 (tp30) cc_final: 0.6758 (tp30) REVERT: C 265 GLN cc_start: 0.9134 (mt0) cc_final: 0.8878 (mp10) REVERT: C 793 ASP cc_start: 0.8660 (m-30) cc_final: 0.8421 (t0) REVERT: C 794 LYS cc_start: 0.8868 (tptp) cc_final: 0.8466 (tppp) REVERT: D 265 GLN cc_start: 0.9135 (mt0) cc_final: 0.8874 (mp10) REVERT: D 793 ASP cc_start: 0.8662 (m-30) cc_final: 0.8426 (t0) REVERT: D 794 LYS cc_start: 0.8880 (tptp) cc_final: 0.8358 (tppp) REVERT: D 795 GLU cc_start: 0.8506 (mp0) cc_final: 0.7935 (mp0) outliers start: 18 outliers final: 17 residues processed: 189 average time/residue: 0.1814 time to fit residues: 49.4833 Evaluate side-chains 181 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.101685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089571 restraints weight = 34156.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091357 restraints weight = 23859.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092694 restraints weight = 17849.673| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9288 Z= 0.228 Angle : 0.900 12.994 12480 Z= 0.438 Chirality : 0.049 0.344 1420 Planarity : 0.004 0.031 1612 Dihedral : 4.742 18.152 1248 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.87 % Allowed : 22.05 % Favored : 76.08 % 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: -0.66 (0.25), residues: 1128 helix: 1.15 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.47 (0.21), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 169 PHE 0.008 0.001 PHE D 193 TYR 0.019 0.001 TYR A 72 ARG 0.012 0.001 ARG D 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.99 seconds wall clock time: 35 minutes 50.21 seconds (2150.21 seconds total)