Starting phenix.real_space_refine on Mon Sep 23 13:49:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqq_13596/09_2024/7pqq_13596.cif" } resolution = 3.3 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= 0.015 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 31 5.16 5 C 2105 2.51 5 N 516 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2279 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 281} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Time building chain proxies: 2.73, per 1000 atoms: 0.85 Number of scatterers: 3207 At special positions: 0 Unit cell: (56.448, 81.648, 96.768, 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 31 16.00 O 555 8.00 N 516 7.00 C 2105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 793 " - pdb=" SG CYS B 866 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 391.7 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 57.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.955A pdb=" N SER A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.533A pdb=" N ILE A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.542A pdb=" N LYS A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 4.588A pdb=" N ILE A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.788A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.506A pdb=" N SER A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 111' Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.519A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.551A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 4.240A pdb=" N ILE A 174 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 210 removed outlier: 4.208A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.081A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.527A pdb=" N ALA A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.777A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.693A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.737A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.505A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 307 removed outlier: 4.486A pdb=" N LEU A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 883 removed outlier: 3.941A pdb=" N LEU B 882 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.777A pdb=" N LEU B 791 " --> pdb=" O LEU B 851 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.773A pdb=" N TRP B 806 " --> pdb=" O VAL B 818 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 820 " --> pdb=" O MET B 804 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET B 804 " --> pdb=" O PHE B 820 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 803 " --> pdb=" O ALA B 869 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.773A pdb=" N TRP B 806 " --> pdb=" O VAL B 818 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 820 " --> pdb=" O MET B 804 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET B 804 " --> pdb=" O PHE B 820 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 803 " --> pdb=" O ALA B 869 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 402 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: 0.80 Time building geometry restraints manager: 0.91 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: 971 1.34 - 1.46: 755 1.46 - 1.58: 1499 1.58 - 1.70: 0 1.70 - 1.81: 49 Bond restraints: 3274 Sorted by residual: bond pdb=" C ARG A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.68e+00 bond pdb=" CB VAL B 834 " pdb=" CG2 VAL B 834 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.59e-02 3.96e+03 1.19e+00 bond pdb=" CB VAL B 894 " pdb=" CG2 VAL B 894 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.13e-01 bond pdb=" C PHE A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.329 1.339 -0.009 1.18e-02 7.18e+03 6.36e-01 ... (remaining 3269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 4285 1.59 - 3.18: 128 3.18 - 4.77: 16 4.77 - 6.36: 8 6.36 - 7.95: 2 Bond angle restraints: 4439 Sorted by residual: angle pdb=" N ILE A 161 " pdb=" CA ILE A 161 " pdb=" C ILE A 161 " ideal model delta sigma weight residual 113.00 109.11 3.89 1.30e+00 5.92e-01 8.97e+00 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 120.65 -7.95 3.00e+00 1.11e-01 7.03e+00 angle pdb=" NE ARG B 815 " pdb=" CZ ARG B 815 " pdb=" NH1 ARG B 815 " ideal model delta sigma weight residual 121.50 119.01 2.49 1.00e+00 1.00e+00 6.18e+00 angle pdb=" N PRO A 15 " pdb=" CA PRO A 15 " pdb=" C PRO A 15 " ideal model delta sigma weight residual 110.70 113.16 -2.46 1.22e+00 6.72e-01 4.08e+00 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 123.19 -6.89 3.50e+00 8.16e-02 3.88e+00 ... (remaining 4434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 1705 15.89 - 31.78: 186 31.78 - 47.67: 50 47.67 - 63.56: 5 63.56 - 79.46: 2 Dihedral angle restraints: 1948 sinusoidal: 750 harmonic: 1198 Sorted by residual: dihedral pdb=" CA PHE A 274 " pdb=" C PHE A 274 " pdb=" N PRO A 275 " pdb=" CA PRO A 275 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE A 304 " pdb=" C PHE A 304 " pdb=" N TRP A 305 " pdb=" CA TRP A 305 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU B 814 " pdb=" CB GLU B 814 " pdb=" CG GLU B 814 " pdb=" CD GLU B 814 " ideal model delta sinusoidal sigma weight residual -60.00 -114.43 54.43 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 284 0.028 - 0.057: 165 0.057 - 0.085: 55 0.085 - 0.113: 22 0.113 - 0.142: 4 Chirality restraints: 530 Sorted by residual: chirality pdb=" CB VAL B 834 " pdb=" CA VAL B 834 " pdb=" CG1 VAL B 834 " pdb=" CG2 VAL B 834 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO B 858 " pdb=" N PRO B 858 " pdb=" C PRO B 858 " pdb=" CB PRO B 858 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL A 154 " pdb=" N VAL A 154 " pdb=" C VAL A 154 " pdb=" CB VAL A 154 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 527 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 825 " -0.010 2.00e-02 2.50e+03 1.23e-02 3.01e+00 pdb=" CG TYR B 825 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 825 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 825 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 825 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 825 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 825 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 825 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 838 " 0.001 2.00e-02 2.50e+03 1.05e-02 1.92e+00 pdb=" CG PHE B 838 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 838 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 838 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 838 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 838 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 838 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 244 " -0.008 2.00e-02 2.50e+03 9.87e-03 1.70e+00 pdb=" CG PHE A 244 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 244 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 244 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 244 " -0.001 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 710 2.78 - 3.31: 3155 3.31 - 3.84: 4893 3.84 - 4.37: 6108 4.37 - 4.90: 10318 Nonbonded interactions: 25184 Sorted by model distance: nonbonded pdb=" O ALA A 111 " pdb=" NE1 TRP A 305 " model vdw 2.244 3.120 nonbonded pdb=" O ASN A 17 " pdb=" NZ LYS A 20 " model vdw 2.290 3.120 nonbonded pdb=" N ASP A 115 " pdb=" OG1 THR A 253 " model vdw 2.431 3.120 nonbonded pdb=" N GLY A 19 " pdb=" OD2 ASP A 24 " model vdw 2.438 3.120 nonbonded pdb=" OG1 THR A 13 " pdb=" N LEU A 14 " model vdw 2.478 3.120 ... (remaining 25179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.045 3274 Z= 0.241 Angle : 0.685 7.954 4439 Z= 0.368 Chirality : 0.041 0.142 530 Planarity : 0.004 0.032 540 Dihedral : 14.020 79.456 1179 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -2.50 (0.40), residues: 411 helix: -1.59 (0.36), residues: 194 sheet: -1.56 (0.81), residues: 40 loop : -1.58 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 823 HIS 0.001 0.000 HIS A 54 PHE 0.023 0.002 PHE A 244 TYR 0.031 0.003 TYR B 825 ARG 0.005 0.001 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.358 Fit side-chains REVERT: A 72 MET cc_start: 0.7274 (mmm) cc_final: 0.7008 (mmp) REVERT: A 228 LEU cc_start: 0.8634 (tp) cc_final: 0.8225 (tt) REVERT: A 257 GLU cc_start: 0.7612 (tp30) cc_final: 0.7402 (tp30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1266 time to fit residues: 16.0417 Evaluate side-chains 89 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN B 824 ASN B 888 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3274 Z= 0.254 Angle : 0.680 7.239 4439 Z= 0.337 Chirality : 0.042 0.138 530 Planarity : 0.005 0.035 540 Dihedral : 4.867 21.703 447 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.83 % Allowed : 14.73 % Favored : 82.44 % 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: -2.41 (0.39), residues: 411 helix: -1.52 (0.34), residues: 203 sheet: -1.49 (0.79), residues: 40 loop : -1.52 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 PHE 0.020 0.002 PHE A 128 TYR 0.015 0.003 TYR A 238 ARG 0.003 0.001 ARG B 837 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.344 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1186 time to fit residues: 13.4957 Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3274 Z= 0.224 Angle : 0.640 8.047 4439 Z= 0.311 Chirality : 0.041 0.133 530 Planarity : 0.005 0.037 540 Dihedral : 4.600 20.623 447 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.68 % Allowed : 16.71 % Favored : 79.60 % 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: -2.19 (0.39), residues: 411 helix: -1.28 (0.35), residues: 201 sheet: -1.36 (0.80), residues: 39 loop : -1.51 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 PHE 0.015 0.002 PHE A 128 TYR 0.013 0.002 TYR A 186 ARG 0.002 0.000 ARG B 837 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.355 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1256 time to fit residues: 14.3133 Evaluate side-chains 92 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3274 Z= 0.265 Angle : 0.650 7.741 4439 Z= 0.321 Chirality : 0.042 0.130 530 Planarity : 0.005 0.035 540 Dihedral : 4.617 19.914 447 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.53 % Allowed : 19.83 % Favored : 75.64 % 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: -2.13 (0.40), residues: 411 helix: -1.23 (0.35), residues: 200 sheet: -1.29 (0.76), residues: 46 loop : -1.48 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 PHE 0.015 0.002 PHE B 817 TYR 0.015 0.002 TYR A 186 ARG 0.003 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.322 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.1178 time to fit residues: 13.5047 Evaluate side-chains 90 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3274 Z= 0.409 Angle : 0.759 10.115 4439 Z= 0.377 Chirality : 0.045 0.149 530 Planarity : 0.005 0.033 540 Dihedral : 4.992 20.263 447 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.97 % Allowed : 23.80 % Favored : 72.24 % 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: -2.40 (0.39), residues: 411 helix: -1.30 (0.35), residues: 196 sheet: -1.88 (0.71), residues: 52 loop : -1.65 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.001 0.000 HIS A 54 PHE 0.020 0.002 PHE B 817 TYR 0.020 0.003 TYR A 186 ARG 0.003 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.838 Fit side-chains REVERT: A 89 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7289 (mt-10) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.1842 time to fit residues: 20.9628 Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3274 Z= 0.177 Angle : 0.619 9.164 4439 Z= 0.300 Chirality : 0.040 0.131 530 Planarity : 0.004 0.035 540 Dihedral : 4.481 19.426 447 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.67 % Allowed : 22.10 % Favored : 72.24 % 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: -2.03 (0.40), residues: 411 helix: -1.11 (0.35), residues: 198 sheet: -1.39 (0.80), residues: 46 loop : -1.42 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 886 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.001 PHE A 292 TYR 0.013 0.002 TYR B 883 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.355 Fit side-chains REVERT: A 288 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8539 (tp) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.1139 time to fit residues: 13.5495 Evaluate side-chains 94 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 11 optimal weight: 0.0060 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3274 Z= 0.161 Angle : 0.614 8.689 4439 Z= 0.293 Chirality : 0.040 0.130 530 Planarity : 0.004 0.036 540 Dihedral : 4.294 18.229 447 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.97 % Allowed : 23.51 % Favored : 72.52 % 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: -2.02 (0.39), residues: 411 helix: -1.04 (0.35), residues: 199 sheet: -1.56 (0.82), residues: 39 loop : -1.48 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 886 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.001 PHE A 292 TYR 0.012 0.001 TYR B 883 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.365 Fit side-chains REVERT: A 72 MET cc_start: 0.7209 (mmm) cc_final: 0.6936 (mmp) REVERT: A 285 PHE cc_start: 0.8294 (t80) cc_final: 0.7989 (t80) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.1251 time to fit residues: 14.1421 Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3274 Z= 0.144 Angle : 0.614 9.136 4439 Z= 0.287 Chirality : 0.039 0.128 530 Planarity : 0.004 0.037 540 Dihedral : 4.104 16.811 447 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.12 % Allowed : 23.80 % Favored : 73.09 % 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: -2.00 (0.40), residues: 411 helix: -0.97 (0.35), residues: 200 sheet: -1.40 (0.81), residues: 39 loop : -1.58 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 886 HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE A 292 TYR 0.011 0.001 TYR B 883 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.359 Fit side-chains REVERT: A 72 MET cc_start: 0.7310 (mmm) cc_final: 0.7054 (mmp) REVERT: A 112 MET cc_start: 0.7889 (mmm) cc_final: 0.7566 (tpp) REVERT: A 285 PHE cc_start: 0.8236 (t80) cc_final: 0.7952 (t80) outliers start: 11 outliers final: 11 residues processed: 88 average time/residue: 0.1262 time to fit residues: 13.9103 Evaluate side-chains 87 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 0.0030 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3274 Z= 0.153 Angle : 0.614 9.171 4439 Z= 0.290 Chirality : 0.039 0.129 530 Planarity : 0.004 0.036 540 Dihedral : 4.059 16.071 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.12 % Allowed : 23.80 % Favored : 73.09 % 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: -1.73 (0.40), residues: 411 helix: -0.67 (0.36), residues: 192 sheet: -1.30 (0.80), residues: 39 loop : -1.53 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 823 HIS 0.001 0.000 HIS A 54 PHE 0.010 0.001 PHE A 292 TYR 0.011 0.001 TYR B 883 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.353 Fit side-chains REVERT: A 257 GLU cc_start: 0.7717 (tp30) cc_final: 0.7350 (tp30) REVERT: A 285 PHE cc_start: 0.8237 (t80) cc_final: 0.7969 (t80) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.1289 time to fit residues: 13.9043 Evaluate side-chains 88 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3274 Z= 0.173 Angle : 0.618 8.779 4439 Z= 0.294 Chirality : 0.039 0.130 530 Planarity : 0.004 0.036 540 Dihedral : 4.059 15.107 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 24.65 % Favored : 72.24 % 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: -1.57 (0.40), residues: 411 helix: -0.49 (0.37), residues: 192 sheet: -1.30 (0.79), residues: 39 loop : -1.49 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 305 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.001 PHE A 292 TYR 0.012 0.002 TYR A 69 ARG 0.003 0.000 ARG B 829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.342 Fit side-chains REVERT: A 257 GLU cc_start: 0.7604 (tp30) cc_final: 0.7380 (mm-30) REVERT: A 285 PHE cc_start: 0.8250 (t80) cc_final: 0.7961 (t80) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.1313 time to fit residues: 13.9625 Evaluate side-chains 89 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.0000 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 14 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148914 restraints weight = 4960.929| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.74 r_work: 0.3810 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3274 Z= 0.149 Angle : 0.603 8.924 4439 Z= 0.285 Chirality : 0.039 0.129 530 Planarity : 0.004 0.036 540 Dihedral : 3.910 14.098 447 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 24.65 % Favored : 72.24 % 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: -1.45 (0.40), residues: 411 helix: -0.31 (0.37), residues: 189 sheet: -1.26 (0.79), residues: 39 loop : -1.51 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.001 PHE A 292 TYR 0.010 0.001 TYR B 883 ARG 0.003 0.000 ARG B 829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.19 seconds wall clock time: 23 minutes 7.42 seconds (1387.42 seconds total)